National Electrofishing Programme for Scotland (NEPS) 2023: status of juvenile Atlantic salmon and brown trout populations

Introduction

Diadromous fish populations (those migrating between marine and freshwater environments) are sentinels of change at global and local levels (Soulsby et al., 2024) and are thus susceptible to a wide range of pressures in marine and freshwater environments (Limburg and Waldman, 2009; Almeida et al., 2023). Atlantic salmon (Salmo salar) (hereafter salmon) are a species of high economic, conservation and cultural importance that are protected by international management agreements (North Atlantic Salmon Conservation Organisation; NASCO) and legislation at national (e.g. The Conservation of Salmon (Scotland) Regulations) and international levels (Conservation of Habitats and Species (Amendment) (EU Exit) Regulations 2019). Brown trout (Salmo trutta) (hereafter trout), exhibit a wide range of life history strategies including freshwater resident and anadromous forms (sea trout), and are a UK Biodiversity Action Plan priority fish species. At the last valuation, wild freshwater fisheries, which are dominated by salmon and trout, were estimated to account for around £79.9m Gross Value Added (GVA) to the Scottish economy each year, supporting ca. 4,300 full-time equivalent jobs (PACEC, 2017).

Despite their importance, salmon (Chaput, 2012; ICES, 2024a) and sea trout (Jutila et al., 2006; Mota et al., 2016; Debowski, 2018; Adams et al., 2022) populations are in decline across much of their native range, and salmon populations in Great Britain were recently reclassified as endangered by the International Union for Conservation of Nature (IUCN). In Scotland, official catch statistics dating back to 1952 report that 2023 was the lowest and fifth lowest rod catch for salmon and sea trout respectively (Marine Directorate, 2024). In response to these declines, fisheries and environmental managers across the north Atlantic have focussed on developing reliable quantitative methods to assess population status (e.g. Alexandre et al. 2025, Malcolm et al., 2019) and the pressures affecting them (e.g. Forseth et al., 2017), to identify and prioritise management actions (Scottish Government, 2023).

Electrofishing data are one of the most commonly collected and accurate sources of information on ecosystem health (Schmutz et al., 2007), population status (Godfrey, 2004; Rivers and Fisheries Trusts Scotland, 2014; Malcolm et al., 2019; HELCOM, 2023; ICES, 2024) and trends (Glover et al., 2019; Douglas et al., 2023; Nunn et al., 2025) in freshwater and diadromous fish species. When collected following consistent protocols, alongside an appropriate survey design, such data have the ability to provide reliable assessments at the wide variety of spatial scales necessary for management and policy decision making, including individual sites (~100m2); sub-catchments, catchments, regions, national (Malcolm et al., 2019b, 2020, 2023) or international scales (ICES. 2024b).

In 2014 a major review was undertaken of freshwater fisheries management in Scotland (Thin et al., 2014). This provided the catalyst for a critical review of existing research, monitoring and assessment methods that were available at the time. As part of this process a working group was established on “juvenile sampling” to determine the availability of existing data and to define research needs and methods required to collect and analyse data suitable for assessing the status of salmon populations in rivers. In 2018 the National Electrofishing Programme for Scotland (NEPS) was established providing the first ever national scale statistical survey of Scotland’s salmon rivers. A new assessment benchmark for salmon was published in 2019 (Malcolm et al., 2019a) followed by the introduction of a new juvenile salmon assessment method (Malcolm et al., 2019b).

In October 2021 the Scottish Government published its response to the Salmon Interactions Working Group (SIWG) report. This included a commitment to extend the NEPS assessment methods to include trout populations. In 2022, the Scottish Government published the Scottish Wild Salmon Strategy (Scottish Government, 2022) with an Implementation Plan following in 2023 (Scottish Government, 2023). The vision outlined in the Wild Salmon Strategy is for flourishing wild salmon populations, which are an example of nature’s recovery, achieved via the application of best practice science and management. The associated implementation plan reiterated the need for a coordinated science and evidence base including monitoring and assessment of juvenile salmon populations. NEPS is an important component of this evidence base providing robust catch independent data on population status and trends and the effects of pressures across nested spatial scales that facilitates management, regulation and policy development.

As fish populations decline, they can exhibit complex compensatory processes that offset expected reductions in freshwater production (Gurney et al., 2008; Soulsby et al., 2024) and result in unexpected changes in spatial habitat use (Gaston et al., 2000). These changes can affect the interpretation of assessment data and decisions on appropriate management actions. The primary focus of NEPS was to provide assessments of the status of juvenile populations, and to identify negatively impacting pressures (e.g. water quality, introgression). However, careful data collection procedures also ensure the development of a dataset that has significant potential to assess other objectives, including an improved understanding of population processes in fresh water.

Previous NEPS publications reported assessment data from 2018, 2019 and 2021, the latter making use of an evolving survey design. This report presents data from 2023 using a further iteration of the NEPS survey design, and as far as possible harmonises these data with earlier surveys to assess changes over time. It also extends reporting to include an assessment of the status of trout for the first time.

Given increasing concerns that low egg deposition (as a function of low spawner numbers) is having marked effects on juvenile salmonid production in some parts of the country, we also consider whether there is evidence of long-term trends in juvenile salmon abundance in three rivers with long term juvenile time series and contrasting NEPS Grade profiles. Finally, we explore relationships between occupancy (proportion of river length containing fish) and abundance, and consider whether there is evidence of changing habitat use and population characteristics in declining populations. This is discussed in the context of population processes, survey and assessment challenges.

The specific objectives of the current report are as follows:

1. Characterise changes in the survey design between the 2018/2019, 2021 and 2023 and the reasons for these changes.

2. Model capture probability for salmon and trout incorporating the latest data from NEPS 2023 and other suitable sources.

3. Report the abundance and status of salmon and trout from the NEPS 2023 survey at site-wise, strata and regional levels.

4. Harmonise temporally varying NEPS survey designs (2018, 2019, 2021, 2023) and associated sample frames to assess spatio-temporal variability in salmon and trout densities, and status across years

5. Assess the effects of river size (Strahler Order) on the densities of salmon and trout and whether inter-annual variability in abundance is consistent across Strahler river orders.

6. Investigate whether three rivers with long term data and different NEPS grades profiles exhibit contrasting trends in juvenile abundance and relationships to proxies of spawner abundance (rod catch).

7. Report on the abundance and status of salmon within SACs and illustrate potential approaches for assessing SAC rivers using juvenile data.

8. Illustrate relationships between prevalence and abundance as an additional indicator of population processes and status.

9. Explore national and regional relationships between juvenile salmonid densities, NEPS grades and rod catch as a proxy of adult abundance.

10. Characterise spatio-temporal variability in water chemistry measurements and discuss how water chemistry might be used as an indicator of water quality pressures to improve the precision of site-wise juvenile assessments.