Appendix 10. Fisheries Surveys

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European bullhead (Cottus gobio), courtesy of James Holloway
Seine netting © Marc-Antoine Colleu

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Scientific best practice

See England et al. (2021) [1]

1. Introduction to fisheries surveys

A large number of techniques are now available to assess fish species and populations. Faced with so many options, managers may wonder which is most suitable to answer their hypotheses and address their catchment’s problems. The techniques outlined here can be used to monitor fish populations before and after river restoration projects. It includes both commonly-used techniques (capture methods such as electrofishing, netting), counting systems (e.g. video-counting, resistivity counter, acoustic camera) and biotelemetry systems (e.g. acoustic or radio telemetry, PIT-tagging); as well as new and less well-known methods (e.g. eDNA, flottang). All the methods can be considered by managers for the utility of the data they can provide.

Recent technological advances have resulted in increasingly efficient methodologies for data capture and processing, improving the monitoring standards for fisheries. A wealth of background information now exists with standardised protocols for sampling and for biotelemetry studies. These improvements mean a greater number of parameters can be recorded and be conducted over larger areas more economically than previously possible. Statistical and informational tools have also improved the accessibility of scientific methods (biotelemetry, metabarcoding). Table 1 provides a summary of all the techniques detailed in this manual, the aim of which is to help managers decide which methods to use to quantify restoration effects. Table 2 provides additional detail for each of the methods outlined in this manual.

It should be noted, however, that all of these techniques have limitations, and to understand complex ecological processes managers may be required to combine several techniques. Here the focus is on methods that can be directly linked with river restoration.

At all times the well-being of fish and preservation of biodiversity must be considered.

To minimise the detrimental effects of sampling it is recommended that statistical methods are used to estimate the minimum number of fish, numbers of sites, and frequency of surveys required to meet the study’s objectives. Fishery assessments must be conducted in accordance with ethical and legal considerations – in England, use of fish capture methods other than licenced rod and line requires consent from the Environment Agency, whilst invasive procedures such as surgical implantation of tags, have to be licenced under the Animals Scientific Procedures Act, administered by the Home Office. In addition, some rare and threatened species have extra protection and additional licences to handle these will be required from Natural England. Invasive procedures (e.g. surgery) must be carried out to a very high standard to ensure the welfare of fish is maintained, reducing risk of biased results arising from poor survival of tagged fish.

General fish handling should also follow best practice principles, which are outlined in, for example, ‘Keepemwet®’ and paying attention to the potential impact of handling behaviour and materials used (Arlinghaus et al., 2007, Gingerich et al., 2007, and Cook et al., 2015).

2. Technique comparison tables

View summary
comparison table
View data
comparison table
View limitation
comparison table

3. Automatic counting systems

Resistive Counter Diagram, © Loughs Agency (2016)

For a long time, automatic counting systems were reduced to resistivity counters. However, some achievement allows now to see fish by recording their movement through filming camera or acoustic camera. The devices used are now being implanted in all sort of configuration like fish ladder, fish by-pass or fish ways but also on more natural rivers by installing barrier to funneled fish. Consistently data are collected and these devices can provide a massive amount of useful data for managers.

Infrared counter

Works by making infrared scans of fish as they enter and leave a narrow channel. Gives information on phenology, i.e. migratory patterns relating to environmental factors (e.g. temperature, flow etc.), and on upstream and downstream migration. Most suitable for monitoring migratory salmonids, often used in conjunction with video in order to validate and identify fish species. Could be used to assess fish migration and abundance before and after ecological continuity restoration work, e.g. fishway, bypass, dam or weir removal.

Resistivity counter

Works by measuring the change in the resistivity of water flowing through a specially built channel when a fish swims through it. Gives information on phenology, i.e. migratory patterns relating to environmental factors (e.g. temperature, flow etc.), and on upstream and downstream migration. Most suitable for monitoring migratory salmonids, often used in conjunction with video in order to validate and identify fish species. Can be used to assess fish migration and abundance before and after ecological continuity restoration work, e.g. fishway, bypass, dam or weir removal.
Find out more about resistivity counters

Video-counting systems and underwater observation rooms

Equipment can be installed on existing fish passes or by diverting some or all of the river flow through a specially-built channel. Can provide quantitative estimates of numbers of migrating fish, such as adult salmon and trout, as well as other information such as age, size, species and condition of fish. Can be used to assess fish community and density before and after ecological continuity restoration work, e.g. fishway, bypass or dam removal.
Find out more about video-counting systems // Find out more about underwater observation rooms

4. Capture techniques

Electrofishing run © Judy England, Environment Agency

Electric fishing

Can provide either qualitative, semi-quantitative, or quantitative data on fish population at a local scale (10’s m to 100’s m). Single or timed electrofishing passes provide qualitative estimates, whereas multiple passes, ideally delimited by stop nets, provide more quantitative estimates. Fish species, number, length, and weight should be recorded to allow accurate evaluations of population change. Can be used from bank (most effective in wadeable streams), boat (non-wadeable rivers) or portable backpack (small streams). Tagging or scale sampling can be done simultaneously. Can provide information on habitat use, densities, biomasses, population age and size structure, growth rates and fish community composition before and after river restoration and habitat enhancement projects.
Find out more about electric fishing

Flottang

Monitors young eels (<15 cm) on their way upstream during stream colonization and in marshland where electrofishing cannot be used(due to salinity or depth). For ecological continuity restoration, marshland connection and habitat use in restored rivers.
Find out more about Flottang

Fyke net

Fyke netting is a passive method relying on fish swimming into the net and becoming trapped. It can estimate relative fish abundance and their habitat use (in marshland, for example) and movement patterns. This technique is size selective according to the mesh size selected. It is also species-selective, and provides only an indication of fish assemblages. Best suited for downstream migratory species (e.g. adult eels) or benthic species, and is useful in complex habitats where active methods may be impractical. Useful in ecological continuity restoration, reconnection of river and marshland.
Find out more about fyke nets

Gill net

Setting a seine net within stop nets. Source: Environment Agency

A 'passive' fish capture method in which fish encounter and become entangled in fine mesh. Gillnets can consist of multiple panels of different mesh sizes to catch a range of fish sizes. Can be used to estimate fish relative abundance and a range of other population parameters. Only suitable in larger, deeper rivers. No known examples of use in river restoration since alternative methods are more suitable. It is recommended that the use of gillnets is avoided since they can have a detrimental effect on fish populations especially where rare or valuable species are present.
Find out more about Gill nets

Seine net

Seine netting provides qualitative and quantitative estimates of fish abundance in suitable habitats – generally slow flowing rivers with no obstructions/snags. More suited to studying coarse fish assemblages in lowland rivers. Can provide information on habitat use, densities, biomasses, population age and size structure, growth rates and fish community composition before and after river restoration and habitat enhancement projects.
Find out more about Seine nets

Trap on weir

Trapping is most effective for monitoring migratory species such as adult salmon and trout (usually with fixed-location traps). Quantitative population estimates can be achieved for these species, usually over extensive river lengths. Some traps are designed to capture downstream migrants like smolt or silver-eels, allowing recruitment assessment. Useful to measure population recovery after river continuity restoration or restoration of upstream spawning grounds.
Find out more about traps mounted on weirs

Anglers citizen science

This is a very flexible approach and data can be collected by and from anglers in a number of different ways over varying spatial and temporal timescales. Angling methods can be very selective and data are typically noisy, however they can provide data from diverse environments relatively cheaply. Can provide information on changes in fish abundance, population age and size structure, growth rates, and habitat use, before and after river restoration and habitat enhancement projects.
Find out more about Angler Citizen Science

5. Tracking methods

Pass-through antenna © Scimabio Interfaceg

Telemetry is the process of tagging a fish to track its movements in the river, estuary or sea. This discipline has made a real progress this last decade mainly due to tag reduction size allowing monitoring of a wide range of species and life stages and lead to previously unknown fish behavior (Thorstad et al., 2013). External and internal tags are available. External marks (dart tag, T-bar, self-locking tags) are commonly used in recreational related fishes to get data from citizen science. External tags were almost abandoned because of tissue damage and loss but are now coming back especially under the form of archival (biologging Data Storage Tags DST) and pop-up satellite archival tags (PSATs) (Jepsen et al., 2015) as they are quick to attached especially on non-common shaped fish and can be combined with environmental sensors. However, it seems that internal tags are mostly used for fish tracking in rivers. The recent progress in tag reduction size allow internal tagging with limited drawbacks for fish and few tags expel. Multiple types of telemetry tag (radio, acoustic, PIT) are available today, some of which can receive and transmit data from biotelemetry sensors. These tools furnish unattainable data using other techniques and are valuable for conservation practitioners (Cooke, 2008).

Acoustic camera, multibeam sonar

A versatile system which can be deployed in a number of ways, by converting high resolution acoustic signals into a visual output resembling a plan view of a section of river bed and the fish swimming above it. It’s non-invasive. Units can be mounted on bank or boat and the system can be used to survey at night, in turbid water, or amongst underwater obstructions and macrophytes. Can discern timing and extent of movements of different class sizes and species of fish relating to environmental factors, at high spatial and temporal resolution. Can be used to assess fish abundance in absolute or relative terms, habitat utilisation and detailed fish behaviour.
Find out more about acoustic camera methods

Acoustic telemetry

Operates using surgically-implanted tags which produce sound signals, in conjunction with hand held and fixed receivers. Useful to evaluate ecological continuity following restoration work (e.g. fishway, bypass, dam or weir removal) fish behaviour and habitat utilisation.
Find out more about acoustic telemetry

Coded wire tags/visible implant tags

Coded Wire Tags are very tiny metal tags inserted just under the fish’s skin and registered when the fish is re-captured using a hand-held reader. It allows identification of individual fish and so can be used to provide information on migration, growth etc. Typically used in Mark-Recapture experiments to monitor large numbers of fish. Sometimes used in conjunction with other identification methods. Can be used as evidence of ecological continuity restoration and success of habitat restoration.
Find out more about coded wire tags

Radio Frequency Identification – PIT Tag

Operates by propagation of radio waves that activate coded tags surgically implanted in fish. Provides data on accessibility and passability of fishways. Can be used for population estimates with mark-recapture protocol and provides individual fish identification, enabling more detailed information on migration and movement relative to specific locations, as the system has very limited spatial range. Applicable to a wide range of species and sizes of fish. Good for studying behaviour around weirs, obstacles, and culverts. Useful to evaluate ecological continuity restoration work (fishway, bypass, dam/weir removal).
Find out more about RFID - PIT Tags

Radio telemetry

Uses radio tags, implanted or attached to individual fish, which transmit radio waves of specific frequencies that can be detected by fixed or hand-held receivers. Used to evaluate fish migration, presence on spawning grounds, habitat utilization, in addition to fish behaviour on the home range or over longer stretches of river. Useful to evaluate ecological continuity restoration work (fishway, bypass, dam/weir removal), fish behaviour and habitat utilisation.
Find out more about radio telemetry

6. Other

Atlantic salmon Salmo salar redd and individual – Allier river @ LOGRAMI

Lamprey ammocoete sampler

Used to sample ammocoetes (only effective for stage 0+ ammocoetes, i.e. individuals less than <40 mm in length) without electrofishing. Can be used to estimate the recruitment and identify nursery areas for Lampetra fluviatilis, Lampetra planeri and sometimes sea lamprey (Petromyzon marinus). For ecological continuity restoration and habitat restoration.
Find out more about Lamprey ammocoete samplers

Redd counting

Gives data on the number of redds in a stream portion. Useful for identifying fish spawning grounds in the case of river continuity restoration, can also be used to assess spawner abundance.
Find out more about Redd counting

Snorkeling

Provides quantitative estimation on density, relative abundance, spatial distribution, size and structure of a fish population by transects or habitat targeted campaigns. Usually applied to reaches of >100 m. Effective but time consuming. Can determine habitat use, densities, and fish communities (but non-exhaustive) after river restoration projects and habitat enhancement.
Find out more about snorkeling

7. References

Arlinghaus, R. et al. (2007)
Fish welfare: A challenge to the feelings-based approach, with implications for recreational fishing, Fish and Fisheries, 8(1), pp. 57–71. doi: 10.1111/j.1467-2979.2007.00233.x.
Cook, K. V. et al. (2015)
Un poisson hors de l’eau: Quelle est la quantité d’air maximale admissible?, Fisheries, 40(9), pp. 452–461. doi: 10.1080/03632415.2015.1074570.
Cooke, S. J. (2008)
Biotelemetry and biologging in endangered species research and animal conservation: Relevance to regional, national, and IUCN Red List threat assessments, Endangered Species Research, 4(1–2), pp. 165–185. doi: 10.3354/esr00063.
Cooke, S. J. et al. (2008)
Developing a Mechanistic Understanding of Fish Migrations by Linking Telemetry with Physiology, Behavior, Genomics and Experimental Biology: An Interdisciplinary Case Study on Adult Fraser River Sockeye Salmon, Fisheries, 33(7), pp. 321–339. doi: 10.1577/1548-8446-33.7.321.
Cowx, I. G., and Fraser, D. (2003)
Monitoring the Atlantic Salmon. Conserving Natura 2000 Rivers Monitoring Series No. 7, English Nature, Peterborough.
Cowx, I. G., and Harvey, J. P. (2003)
Monitoring the Bullhead, Cottus gobio. Conserving Natura 2000 Rivers Monitoring Series No. 4, English Nature, Peterborough.
DVWK (2002)
Monitoring of fish passes, in Fish passes – Design, dimensions and monitoring, 103-106.
Gingerich, A. J. et al. (2007)
Evaluation of the interactive effects of air exposure duration and water temperature on the condition and survival of angled and released fish, Fisheries Research, 86(2–3), pp. 169–178. doi: 10.1016/j.fishres.2007.06.002.
Harvey, J. P., and Cowx, I. G. (2003)
Monitoring the River, Brook and Sea Lamprey, Lampetra fluviatilis, L. planeri and Petromyzon marinus. Conserving Natura 2000 Rivers Monitoring Series No. 5, English Nature, Peterborough.
Jepsen, N. et al. (2015)
The use of external electronic tags on fish: An evaluation of tag retention and tagging effects, Animal Biotelemetry. BioMed Central, 3(1). doi: 10.1186/s40317-015-0086-z.
JNCC, (2003)
Monitoring White-clawed Crayfish, Austropotamobius. Conserving Natura 2000 Rivers Monitoring Series No. 1, English Nature, Peterborough.
JNCC, (2003)
Monitoring Freshwater Pearl Mussell, Margaritifera margaritifera. Conserving Natura 2000 Rivers Monitoring Series No. 2, English Nature, Peterborough.
JNCC, (2003)
Monitoring Allis and Twaite Shad, Alosa alosa and A. fallax. Conserving Natura 2000 Rivers Monitoring Series No. 3, English Nature, Peterborough.
Thorstad, E. B. et al. (2013)
The Use of Electronic Tags in Fish Research - An Overview of Fish Telemetry Methods, Turkish Journal of Fisheries and Aquatic Sciences, 13(January), pp. 881–896. doi: 10.4194/1303-2712-v13.
Travade, F., and Larinier, M. (2002)
Monitoring techniques for fishways, in Fishways: biological basis, design criteria and monitoring, 166-180.