An outline plan of scientific work is proposed for the Trust to consider.

The aim of the Plan is to acquire the knowledge necessary to manage the fish populations of the Flow Country and the fisheries they support. The target should be to manage in the best practicable fashion, taking account of the wider ecological and land management settings in which the fish populations exist. The Plan will strengthen the basis on which to argue for the interests of the fisheries and, when necessary, to suggest management actions to improve fisheries or compensate for adverse effects.

An initial five year plan is proposed, recognising that a substantial amount of work is required to gain a sufficient understanding of all the main issues. Furthermore, many changes are long-term in nature and many aspects of change are seasonal limiting opportunities for data gathering to a brief period in any year.

The suggested approach is to support and fund a modest autonomous programme, collaborate with others on projects of mutual interest and, more generally, encourage and facilitate activities of the scientific community in researching those aspects of the Flow Country that impinge on its lochs and rivers. The Plan therefore ought to include scope to respond to emergent issues or opportunities when they arise.

At this stage, the main up-coming issues for the Flow Country rivers can be identified as -



Alan F. Youngson

A provisional list of proposed projects is discussed in what follows. For ease of reference they are listed below. All the projects link in various ways to the five themes listed above.


Public bodies such as SEPA, SNH and Marine Scotland Science (MSS) collect data for all the Scottish rivers, including those of the Flow Country. Notably, SEPA monitors river height across a range of locations and has seven gauging sites in the Trust’s area that continuously monitor flow (1). In yet other cases, data is collected in response to specific local needs. For example, SNH obtains electric-fishing data for salmon SACs, including those in the Flow Country, but only on a five year cycle. Much of the data is publically available but often the scale of collection or the frequency of sampling is insufficient to address issues that are locally important. The Trust should therefore aim to fill some of the gaps or encourage others to do so.

The following projects cover important areas. The resources required are likely to be beyond the Trust’s reach but they could be achieved by collaborating with scientists working for other organisations with shared interests.

(1) http://www.sepa.org.uk/water/river_levels/river_level_data.aspx?sm=t&ex=-56900,%20423793,%20604560,%201270461

1a. Stream temperature. A trend towards increasing stream temperature is likely to become increasingly important in coming years. High temperatures have the potential to affect both juvenile and adult salmon, as well as other fish and non-fish species. Many of the Flow Country rivers are spate rivers and, therefore, particularly susceptible to warming at times of low flow. Indeed, unusually high temperatures have already been recorded in the Flow Country rivers and the 2013 survey of the Caithness rivers showed that such effects are adversely affecting young fish. Equally, the effect of low water and high temperature is not uniformly evident and some fish and some locations appear to be more susceptible than others.

MSS is initiating a programme to monitor temperatures across the Scottish rivers, to find out how the response to warming varies among locations and to determine why this is. The Thurso is listed among the chosen set of Scottish rivers because of its location and characteristics. The Trust should facilitate work like this. It should also respond by contributing fish data of the type obtained for the Caithness rivers in 2013 in order to aid interpretation by linking data on fish performance with temperature.

However, MSS is a national organisation and its remit is correspondingly wider than the Trust’s. If necessary, the Trust should therefore take steps to augment MSS’ collection of temperature data in order to ensure that its own requirement for local information is met.

The aims of this programme would be to establish the magnitude, frequency and distribution of episodes of high temperature and to determine which locations and types of location are most susceptible - all as a prelude to considering what measures might be available for mitigation.

1b. Stream chemistry. Many aspects of land management have the potential to adversely affect stream chemistry to the detriment of fish and other species. In the Flow Country catchments, forest clearance, re-planting and peatland modification are likely to be major activities in coming years. All are likely to result in transient or long-term changes to water quality (including sediment input) that are potentially unfavourable for aquatic species. Changes of this type tend to be extremely complex and context-specific because of the interplay of chemistry with topography, soils and weather. Moreover, measurement of chemical parameters is a technical area best dealt with by specialist laboratories and therefore beyond the reach of the Trust.

Again, however, the Trust should encourage and facilitate the work of other parties in this area. In addition, because of its local presence, the Trust can play a special role in obtaining water samples for analysis. For example, strategic sampling during the brief periods of floodwater is important because many changes in water chemistry become particularly evident under these conditions. This form of sampling is sometimes best organised locally by people on the ground who are in a position to respond quickly to transient events.

1c. The smolt migration. Although the Trust’s remit is effectively restricted to juvenile salmonids and to fresh water because of the immense resources required to perform marine research, there are aspects of the transitional phase between freshwater and marine life of juvenile salmonids that are important and potentially accessible.  These relate to behaviour at smolting and during the early stage of marine life and they are particularly important in the context of marine renewables development.

First, the migration of smolts and their entry to the sea is considered to take place around May. However, this timing is only generally defined and although river managers gain an impression from their observations, no specific information exists for the Flow Country rivers.  Knowledge of timing is necessary for mitigation, for example, during construction works; potentially disruptive operations such as pile-driving can be timed to avoid sensitive periods when these are known.

Temporary smolt-wheel traps can be used to capture migrant smolts enabling timings to be defined. In addition, smolt trapping would produce information on body size and age (from scale reading) that would complement electric-fishing survey information obtained earlier in the life-cycle.

Secondly, the Pentland Firth and its environs will be central to marine renewables development because the extreme sea conditions that prevail there represent an intense and relatively consistent source of power.  Indeed, tidal flows in the Firth are so rapid that they must totally dominate the movements of any young fish that attempt to move through because the speed of the currents is so much greater than the swimming capacity of the fish. As is well-known, there is a risk that marine turbines or wave energy converters will add addition risks to any smolts in the vicinity as they transit to their feeding grounds in the northern ocean.

A glance at the map, however, suggests that smolts leaving the various Flow Country rivers will not be affected in the same ways or to the same extent. Thus, for example, smolts leaving the Thurso or Naver need not enter the Pentland Firth to make their journey, especially if they initially head westwards and close inshore.  However, for smolts leaving the Wick or Berriedale, for example, the risks appear to be much greater because the Pentland Firth is an obvious candidate route north and westwards towards the feeding grounds. These same considerations are likely to relate to any of the developments that are planned and to any future proposals because, perhaps paradoxically, the proximity of the Flow Country rivers to the developments increases the likelihood that their migrants will be differently affected. Unfortunately, there is no information on the actual routes used by smolts leaving the Flow Country rivers or, indeed, any other rivers, and this is a critical knowledge gap.

MSS is currently planning a programme to study the outwards movement of smolts in coastal waters. Although the details of this work have not been finalised the approach is likely to centre on using arrays of listening stations to follow smolts tagged with acoustic transmitters. The resources required to mount such an operation are very large and it is therefore unlikely that any programme will be sufficiently extensive to generate the local information the Trust needs.

Active tracking – by which smolts tagged with acoustic transmitters are followed from a boat using a hand-held acoustic receiver – is challenging but technically feasible and the associated costs are likely to be less. Active tracking is potentially suited to getting fine-grain information on the initial marine routes of small numbers of individuals - even if work is only possible for short periods and in good weather. The downside is that active tracking places a huge premium on the skills and tenacity of those involved.

Because of the importance of this work and its difficulty, the Trust should seek collaboration, making facilities and fish available and supporting the specialists who might carry out such work. Active tracking has the potential to provide an understanding of the scope for interaction between smolts and renewables, particularly if the work is repeated across a representative sample of the Flow Country rivers.  If such studies were available they would pinpoint particular areas of concern for the first time and eliminate or downgrade others. This, in turn, would permit a more informed strategic approach to consideration of interactions between fisheries and renewables than is currently possible.

1d. Genetics of salmon and trout. It has become increasingly evident over the past three decades that populations of salmon and other fish species are genetically distinct. This has important knock-on effects for management. In particular, the advent of DNA technology has enabled rapid advances that show that populations differ genetically among locations and that these differences are associated with important effects such as run-timing (the date at which adult or juvenile fish migrate).

In fact, some of this knowledge is not new but rather a re-discovery based on modern technical development. Calderwood, for example, was aware of the differences about 100 years ago based on his own observations of fish and rivers. However, with changing scientific fashion his insights were temporarily lost from view. Only now is the role of genetics in fishery management being properly explored.

Genetic analysis is a specialised technical area and, once again, outside the Trust’s reach. Nevertheless, the Trust should encourage and foster such work. In this spirit, for example, more than 1000 scale samples from salmon obtained in the course of the 2013 electric-fishing survey of the Caithness rivers have been permanently archived (at no cost) as a potential source of DNA and a potential contribution to future genetic study.



It is important to characterise the salmon runs each year because the number of adults and their size determines the number of eggs deposited each year and this is the starting point for the new generation of young fish.

Egg numbers are linked to fry and parr numbers and these, in turn, are linked to smolt numbers; smolt numbers are then linked to the size of the next wave of returning adults and so on. Because all the life stages are interlinked, it is possible to glean useful information on the status of populations at any stage of the life-cycle.  

In recent decades, levels of marine mortality have been unusually high and the resulting decrease in the number of fish returning to the coast has restricted catches and spawner numbers. It is outside the scope of the Trust to address questions around the causes of high marine mortality and, in any case, these matters are being considered by MSS and other bodies.

However, the status of salmon populations can be measured in rivers, as juveniles or as adults. This can be done in a number of ways. None is an infallible guide to population status but each is of value in pinpointing issues for action. Taken together assessment of fish and fisheries in the Flow Country rivers will provide the best available picture on the local scale consistent with the Trust’s remit. Getting good Information on fish and fisheries will form the backbone of the Trust’s work.

The following projects will provide basic information on fish abundance and are probably achievable using only the Trust’s resources.

2a. A juvenile survey programme. Twenty-two sites in the Caithness rivers were examined in 2013 (2) using standard electric-fishing techniques to capture juvenile salmonids and any other fish species present. A new data analysis was developed that appears to be more informative than previous approaches. It provides greater detail and a more integrated picture of salmonid distributions. It also offers a greater understanding of the environmental factors limiting fish density and the biological and environmental controls on these values. The resulting report is therefore a sound starting point for planning future work by the Trust and consolidating information obtained by the Boards for previous years.

(2) http://caithness.dsfb.org.uk/files/2014/05/2013-Survey-of-Juvenile-Salmonids-in-Caithness-Rivers-FINAL.pdf

In future, survey work in the Caithness rivers should be repeated to test and consolidate findings made in 2013. This will confirm the validity of the approach.  It will also allow examination of variation in fish recruitment, growth and performance between years. The Caithness programme should be extended to cover the Flow Country rivers in general. These measures will provide a comprehensive and detailed picture of the fish populations that the rivers support, for the first time.

In addition, the Trust should try to ensure that electric-fishing work performed, for example, by contractors working in support of wind farm developers or for SNH, is completed to a compatible standard and that the results are made publicly available. These data can then also be accommodated in the overall Trust project to add further colour to the picture.

The outcome of these surveys will be a definitive account of the contemporary status of the main target species – salmon - and ancillary data on trout, eels, lampreys, sticklebacks and any other species that may be present in the rivers.  

After the initial phase, a strategic review of the electric-fishing programme should be carried out. This will gauge any need for further routine survey work and any additional needs in the particular context of developments in other areas such as forest management or renewable energy development. Survey work can then be reduced, repeated or extended in future years according to emerging requirements.

2b. Examination of adult catch data. National catch data is already compiled each year by MSS and split down for the formal Fishery Districts but a subsidiary analysis on a river-by-river basis would add more local detail for the Flow Country rivers.

The MSS analysis does not currently include measures of how fishing effort or catch-per-unit effort (fish caught per hour) affects the catch. Nor does it include expert opinion on the presence and catchability of salmon. These measures would be very difficult to enact on the national scale that MSS covers but they could probably be successfully formalised on a local basis for the Flow Country rivers.

In particular, using crude measures of catch-per unit effort (ie. dividing the number of fish caught by the number of anglers fishing) is beset by the problems of trying to compare the effectiveness of occasional anglers with that of professional guides or gillies who have detailed local knowledge and experience. This could be resolved by singling-out habitual fishers and asking them to keep detailed logs of the time they allocate to fishing and the number of fish they catch. This information could be embellished by noting particular features of the fish caught. Measurements of length and information on colouring, condition, presence of sea-lice and sex would be valuable and with appropriate training these features are easily noted, even for fish which are to be released.  

Additionally, all the Flow Country rivers are occasionally beset by factors that reduce catches by hampering both fish and fishermen - for example, by periods of low water. In general, the larger rivers are less affected than the smaller ones. Water level and other effects such as wind direction and light intensity affect the link between measurements of catch-per- unit-effort and the stock of fish in the river - which is the value that managers really need to know.

Expert information on adverse effects on angling success is potentially available from river managers on a river-by-river basis but no previous attempt has been made anywhere to incorporate such information in fishery assessment. Expert assessment could be readily formalised by asking local managers, with a day-to-day impression of the fisheries, to record and interpret their observations, perhaps on a daily basis. Again, this information could be used to qualify and adjust catch-per-unit-effort values and add greater precision and detail to river-by-river assessments by compensating for low catches made in poor fishing conditions.  

2c. Tagging or photographing released fish to estimate stock size. The link between stock size and catch, or catch-per-unit-effort, has been disrupted by the advent of catch-and-release because released fish are re-caught and therefore contribute twice or more to the total catch. A potential solution to this problem is to tag some or all of the released fish in order to calculate recapture rates. This approach has been successfully deployed, for example, on the Spey and the Kyles rivers and similar data already exists for the Naver. It would greatly aid stock assessment and management if tagging was more widely adopted by experienced fishers and ghillies after appropriate technical training.

Alternatively, it may be possible to identify fish captured for a second time from a library of photographs. Young salmon and ferox trout, for example, show patterns of black spots (constellations) on the face which are variable, permanent and unique to individuals. Adult salmon carry fewer spots than young salmon or trout but sufficient to make the identification method worth testing. Therefore, if captured fish were photographed before release it may well be possible to identify them again among fish caught and photographed at a later date.

All that would be required to attempt this is a digital photograph of one side of the face taken from directly above and about 0.5m distant, using a mobile phone or any better camera. This photograph would then be compared with all the fish caught later on in the season to match facial spotting patterns in fish caught for a second time. Measurement of the fish (from tip of snout to fork in tail using a flexible tape measure) would simplify matters by allowing comparison to be restricted to the smaller set of photographs of fish of about the same length.

The procedure would therefore be to measure each fish, obtain a single standard photograph of the left face (raised out of water), specify date and place of capture and confirm that the fish was released. Even more information (unique scars, marks etc) could be provided by also including a full length shot of the left flank. This approach to identification has not been attempted before on adult salmon but it is worth exploring because the photographic method is rather simple. It would also obviate the need for tagging and special training and it would eliminate any logistical problems caused by loss of tags.

The information resulting from either identification method (tagging or photography) could be used to make due allowance for repeat capture of the same fish when considering catches as an indicator of relative stock abundance. In addition, the same information could be used to estimate exploitation rate and therefore to estimate the true total number of fish in the river. This value is usually unknown but it is absolutely crucial for a consideration of whether the number of adults at spawning time matches the capacity of the river to hold young fish.

It may also be possible to establish the sex of fish from photographs, allowing the total number of females to be separately examined. Again, this is potentially valuable information in relation to assessing levels of spawning and egg deposition.



Extensive information on the fisheries and ecology of the Flow Country rivers is available from a wide variety of sources. As yet unidentified sources probably also exist. Some of the readily available sources have a strong historical aspect which it is important to try to understand in order to place the present status of the rivers and their fisheries in a wider context.

Many sources of information have been collected and interpreted in contexts that are not particularly related to fisheries. For example, SEPA has interpreted electric fishing data in the context of the water resource according to its specific remit; SNH has done the same in the context of site condition monitoring of the salmon SACs for rivers like the Thurso and Naver. The Trust should search for and consolidate available sources of information. The data should be brought together and re-interpreted to provide a new account specifically centred on the fisheries.

Both the following projects are achievable using only the Trust’s resources.

3a. Analysis of catch data. MSS has formal catch data for salmon and sea-trout going back to 1952 and this is available to the Trust on a river-by-river basis.  This data should be re-examined to provide an account of the historical development of fisheries on the Flow Country rivers over the period of record.

Summaries of the fisheries reaching even further back are available - for example from the accounts of Grimble and Calderwood at the beginning of the 20th Century. Additional historical information is probably available from such sources as estate and fishery logs or from the business records of the net-fisheries that previously operated in estuaries and coastal waters. These and any other sources that can be identified could be used to provide an historical account of the Flow Country fisheries reaching back beyond the period of the MSS record. An historical account would be used as a basis for comparison of the state of the present-day fisheries, placing contemporary events in a much longer-term setting.

3b. Electric fishing survey data. Although a new start was made with the 2013 survey of the Caithness rivers, it is important to note that extensive survey data exist for previous years for most of the Flow Country rivers. These data should be located and consolidated. They should also be integrated and re-interpreted to provide the best possible account of population status in the years for which they were gathered.



In order to plan the Trust’s work, it will be necessary to identify and take account of information that already exists in order to target effort and avoid duplication. In many cases, the information is dispersed but it should be identified as far as possible and compiled for reference.

All the following projects are probably achievable using only the Trust’s resources.

4a. Ancillary environmental and biological data. Data for the Flow Country’s rivers and lochs - including data on non-salmonid fishes - are available from public sources. For example, SEPA (3) and SNH (4) provide summaries of biological data for rivers and lochs compiled in the context of their respective remits. Again, these and any other data that can be sourced should be consolidated and re-interpreted in the specific context of the fisheries.

(3) http://www.sepa.org.uk/pdf/NH%20catchment%20summaries%20-%20Caithness%20and%20Sutherland.PDF

(4) http://www.snh.gov.uk/docs/A337651.pdf

4b. Previous science projects on Flow Country rivers. The Flow Country rivers have undoubtedly received some attention from scientists In the past but, again, this work is likely to be dispersed. Frost, for example, worked on the feeding ecology of young salmonids in the Forss and published the results as long ago as 1950. In recent years, attention has increasingly focussed on the ecology of the peatlands and this new emphasis is likely to continue. All geographically relevant studies of the Flow Country rivers and their environs should be identified, complied for reference and, thereafter, continuously up-dated.

4c. Trout lochs. Although salmon dominate the Flow Country fisheries, the area contains a myriad of trout lochs. Some support vigorous fisheries and are well-known; many others are visited infrequently or not at all. All of the lochs are part of a valuable ecological resource and the unvisited lochs form part of a potential fishery resource for the future. Many of the lochs probably also contain populations of arctic char - although these generally prove a special technical challenge for the fisherman. Very little is known of these char but they are of immense interest having remained in the same places unseen and undisturbed by man since the last ice-age.

An inventory of lochs should therefore be compiled from contemporary fishery sources and any historical sources that can be identified. For some remote lochs, exploratory fishing may be required to document their fish populations - perhaps for the first time.

4d. Woodland in stream margins. Contemporary forestry practice emphasises the necessity for wide buffer zones along stream and river margins on both aesthetic grounds and as a functional buffer to protect stream chemistry from the potentially adverse effects of forest management. Planting of buffer zones with native trees is often proposed although local species and types are not generally available for use in the extreme North.

Natural woodland is sparse in the Flow Country although this was probably not always the case. Native woodland is currently restricted to the few locations that are not readily accessible to sheep or deer. Nevertheless, steps should be taken to identify relict native or natural woodland where it exists and to establish the range and composition of species present. The upper and eastern parts of the gorge near Dirlot Castle on the Thurso, for example, contains only rowan and birch although planting associated with the old cemetery nearby appears to have affected the tree species in the north-western part of the gorge.

A drift towards naturalistic planting will probably develop, driven by increasing recognition, as for other species, of the importance of conservation genetics in ecology and woodland management. Characterisation of native, stream-side woodland might constitute a preliminary step towards supporting the planting of appropriate native species and types in forest buffer zones along the margins of the Flow Country’s rivers. This approach would be expected to be to the greater benefit of dependent species.

In a slightly different context, it is widely predicted that increasing water temperatures will become a potentially adverse feature of northern rivers. Partial shading by marginal tree-planting has been identified as possible mitigation and this is being investigated by fishery interests elsewhere in Scotland. Although it is difficult to envisage planting on the necessary scale in the Flow Country given the existing landscape and existing land-use patterns, an understanding of local, native woodland would prove a sound support for any such work that may prove possible.

4e. Man-made limits on fish production. In some parts of Scotland, industrial and urban development has left a varied legacy of problems for rivers and fish that are only now being addressed. The Flow Country was not much affected by development because of its remoteness and sparse habitation. However, any redundant in-river structures should be identified and, if necessary, consideration should be given to appropriate remedial work.

More generally, the Trust should expect to represent fishery interests in the contexts of structural and engineering works in or near rivers. In many cases, these are expected to comply with official guidance designed to protect fisheries. However, occasion lapses occur or maintenance issues may arise with, for example, culverts. The Trust and its members are well-placed to identify issues that require attention.

In the same way, land-use practices associated with activities such as farming and forestry sometimes result in adverse effects such as sediment influx to streams and rivers or diffuse pollution. Again, the Trust should expect to act as an advocate for the fishery interest in such cases.


The projects listed above are the result of an attempt to provide a balanced programme of work for the Trust. Some projects are listed because they are crucially important for the Trust’s interests. Others are eminently achievable although possibly of lesser importance. Yet others are listed because they offer scope for widespread participation by anyone who is sympathetic to the Trust’s aims.

The intention is that this document will become the Trust’s first Science Plan. Since the issues will quickly become clearer as work progresses, the agreed initial version of the Plan should be reviewed after one year and re-focussed if necessary to constitute the final document.

May 2014

© Alan F. Youngson



1. Strategic acquisition of data.

1a. Stream temperature.

1b. Stream chemistry.

1c. The smolt migration.

1d. Genetics of salmon and trout.

2. New fish and fisheries data.

2a. A juvenile survey programme.

2b. Examination of adult catch data.

2c. Tagging released fish to estimate stock size.

3. Consolidation of existing fisheries data.

3a. Analysis of catch data.

3b. Electric fishing survey data.

4. Inventory of resources.

4a. Ancillary environmental and biological data.

4b. Previous science projects on Flow Country rivers.

4c. Trout lochs.

4d. Woodland in stream margins.

4e. Man-made limits on fish production.