The Central and Regional Fisheries Boards

ACKNOWLEDGEMENTS

The authors wish to gratefully acknowledge the help and co-operation of the Acting CEO Dr. Milton Matthews and the staff of the Northern Regional Fisheries Board. The authors would also like to gratefully acknowledge the help and cooperation from all their colleagues in the Central Fisheries Board and especially Dr. Jimmy King for his guidance with the transitional waters surveys.

We would like to thank the landowners and angling clubs that granted us access to their land and respective fisheries.

We would also like to thank Dr. Martin O’ Grady (CFB) and No. 3 Operational Wing, Irish Air Corps (Aer Chór na hÉireann) for the aerial photographs.

PROJECT STAFF

Project Director/Senior Research officer: Dr. Fiona Kelly Project Manager: Dr. Andrew Harrison Research Officer: Dr. Ronan Matson Research Officer: Ms. Lynda Connor Technician: Ms. Róisín O’Callaghan Technician Ms. Gráinne Hanna Technician Mr. Rory Feeney Technician: Mrs. Ciara Wögerbauer Technician: Ms. Emma Morrissey GIS Officer: Mr. Kieran Rocks

The authors would also like to acknowledge the funding provided for the project from the Department of Communications Energy and Natural Resources for 2009.

The report includes Ordnance Survey data reproduced under OSi Copyright Permit No. MP 007508. Unauthorised reproduction infringes Ordnance Survey Ireland and Government of Ireland copyright. © Ordnance Survey Ireland, 2009

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TABLE OF CONTENTS

1. INTRODUCTION ...... 3

2. METHODS ...... 4

3. RESULTS ...... 5

3.1 Swilly Estuary ...... 5

3.2 Inch Lough ...... 9

4. SUMMARY ...... 12

5. REFERENCES ...... 13

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1. INTRODUCTION

Fish stock surveys were conducted on two transitional water bodies, as part of the programme of fish monitoring for the Water Framework Directive (WFD), between the 7 th and the 14 th of October 2009 by staff from the Central Fisheries Board (CFB) and the Northern Regional Fisheries Board (NRFB) (Table 1.1, Fig. 1.1)).

The Swilly Estuary is located in Co. , on Ireland’s northern coast. Inch Lough is also a part of this estuary, but it is sheltered behind Inch Island, with embankments on either side that have isolated it from the main water body (Fig. 1.1). For the purposes of WFD monitoring and reporting, this large estuary system has been split into two separate water bodies (Table 1.1), further details of which are given in each individual results section.

Table 1.1. Transitional water bodies surveyed for the WFD fish surveillance monitoring programme, October 2009 (TW=transitional, L=Lagoon) Transitional Water body MS Code Easting Northing Type Area (km 2) Lough Swilly NW_220_0100 227873 419149 TW 59.36 Inch Lough NW_220_0300 235199 422986 L 1.63

Fig. 1.1. Location map of the two transitional water bodies in the Swilly Estuary system surveyed for WFD fish monitoring, September 2009

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2. METHODS

Current work in the UK and ROI indicates the need for a multi-method (beach seine, fyke net and beam trawl) approach to sampling fish in estuaries and these procedures are now the standard CFB methodology for fish stock surveys in transitional waters for the WFD monitoring program.

Beach seining is conducted using a 30m x 3m net (10mm mesh size) to capture fish in littoral areas. The bottom of the net has a weighted lead line to increase sediment disturbance and catch efficiency. Fyke nets (15m in length with a 0.8m diameter front hoop, joined by an 8m leader with a 10mm square mesh) are used to sample benthic fish in the littoral areas. Beam trawls are used for sampling benthic fish in the littoral and open waters, where bed type is suitable. The beam trawl measures 1.5m x 0.5m, with a 10mm mesh bag, decreasing to 5mm mesh in the cod end. The trawl is attached to a 20m tow rope and towed by a boat. Trawls are conducted along transects of 100 – 200m in length.

Sample sites are selected to represent the range of geographical and habitat ranges within the water body, based on such factors as exposure/orientation, shoreline slope, and substrate type. A handheld GPS is used to mark the precise location of each site.

All nets are processed on-site by identifying the species present and counting the total numbers caught in each. Length measurements are recorded for each species using a representative sub-sample of 30 fish, while scales are only collected for certain species, such as salmon and sea trout. Unidentified specimens were retained for subsequent identification in the laboratory.

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3. RESULTS

3.1 Swilly Estuary

The Swilly Estuary, also known as Lough Swilly, covers an area of 59.36km² (Figs. 3.1, 3.2 and Plate 3.1). It starts at the tidal limit of the River Swilly in the town of and extends seaward approximately 20km in a north-easterly direction to the village of .

This water body is situated within the Lough Swilly SAC, which contains a number of important habitats, including salt march as well as sand and mud flats. Important species present that are listed in Annex II of the EU Habitats Directive include the otter (NPWS, 2003).

A total of 13 beach seines, 12 beam trawls and eight fyke nets were deployed in the Swilly Estuary in October 2009.

Fig 3.1. Location map of the northern section of the Swilly Estuary indicating sampling sites, October 2009

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Fig 3.2. Location map of the southern section of the Swilly Estuary indicating sampling sites, October 2009

Plate 3.1. Aerial view of the inner part of the Swilly Estuary. The upper channel is mostly mud substrate (Photo courtesy of CFB and No. 3 Operational Wing, Irish Air Corps [Aer Chór na hÉireann])

A total of 32 fish species were recorded in the Swilly Estuary in October 2009 (Table 3.1). Sand goby was the most abundant species captured, followed by sprat, lesser sandeel, plaice and five-bearded

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rockling (Table 3.1). . The Swilly Estuary was the only WFD transitional water body surveyed in 2009 in which common seasnail, sand sole and three-bearded rockling were recorded. Furthermore, greater numbers of eight other species, including lesser spotted dogfish, were captured in the Swilly Estuary than in any other WFD transitional water body surveyed in 2009. Other species of interest included three-spined stickleback, eels and flounder

Plaice ranged in length from 3.1cm to 14.3cm, and their length frequency distribution indicates the sample was predominantly composed of a cohort of juvenile fish (Fig. 3.3). Flounder ranged in length from 4.9cm to 27.2 cm and a similar conclusion can be drawn from the length frequency distribution for this species (Fig. 3.4).

Salinity values taken at each beach seine site ranged from 23.5ppt in the upper estuary to 26.6ppt in the lower estuary.

Table 3.1. Number of each species captured by each gear type in the Swilly Estuary, October 2009

Beach seine Fyke net Beam trawl Scientific name Common Name Total (13) (8) (12) Pomatoschistus minutus Sand goby 1146 - 447 1593 Sprattus sprattus Sprat 692 - 1 693 Ammodytes tobianus Lesser sandeel 625 - - 625 Pleuronectes platessa Plaice 79 5 84 168 Ciliata mustela Five-bearded rockling - 107 1 108 Platichthys flesus Flounder 10 18 16 44 Pollachius pollachius Pollack 1 36 2 39 Callionymus sp Dragonet sp. 5 3 30 38 Pomatoschistus pictus Painted goby 21 - 9 30 Agonus cataphractus Pogge - 11 7 18 Gasterosteus aculeatus Three-spined stickleback 17 - - 17 Spinachia spinachia Fifteen-spined stickleback 13 4 - 17 Trisopterus luscus Bib - 17 - 17 Limanda limanda Dab - - 13 13 Taurulus bubalis Long-spined sea scorpion 3 4 3 10 Gadus morhua Cod - 9 - 9 Trisopterus minutus Poor cod - 9 - 9 Scyliorhinus canicula Lesser spotted dogfish - 8 - 8 Gobius paganellus Rock goby - - 3 3 Atherina presbyter Sand smelt 2 - - 2 Pegusa lascaris Sand sole 2 - - 2 Solea solea Common sole 1 - 1 2 Merlangius merlangus Whiting - 1 1 2 Symphodus melops Corkwing wrasse 1 1 - 2 Anguilla anguilla Eel - 1 - 1 Gaidropsarus vulgaris Three-bearded rockling - 1 - 1 Myoxocephalus scorpius Short-spined sea scorpion - - 1 1 Gobiusculus flavescens Two-spotted goby 1 - - 1 Lipophrys pholis Blenny - 1 - 1 Liparis liparis Common seasnail - 1 - 1 Scyliorhinus stellaris Bull huss - 1 - 1 Raja clavata Thornback ray - - 1 1

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60

50

40

30

Number Number offish 20

10

0 0 2 4 6 8 10 12 14 Length cm

Fig. 3.3. Length frequency distribution of a sub-sample of plaice captured in the Swilly Estuary, October 2009 (n = 157)

8

7

6

5

4

3 Number Number offish 2

1

0 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 Length cm

Fig. 3.4. Length frequency distribution of flounder captured in the Swilly Estuary, October 2009 (n = 44)

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3.2 Inch Lough

Inch Lough is located within the Swilly Estuary on Ireland’s north coast, adjacent to Letterkenny in Co. Donegal and covers an area of 1.63 km² (Fig. 3.5, Plate 3.2). Extensive reclamation in the area has seen the transformation of former intertidal and salt marsh areas to farmland, which is now enclosed by embankments. These embankments have created Inch Lough which is classified as a lagoon due to a partial exchange of water with Lough Swilly at high tide.

This water body is situated within the Lough Swilly SAC, which is described in Section 3.1.

A total of four beam trawls and four fyke nets were deployed in Inch Lough in October 2009.

Fig 3.5. Location map of Inch Lough Estuary indicating sampling sites, October 2009

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Plate 3.2. View of Inch Lough, October 2009.

A total of eight fish species (sea trout are included as a separate ‘variety’ of trout) were recorded in Inch Lough in October 2009 (Table 3.2). Three-spined stickleback was the most abundant species captured, followed by flounder and eel (Table 3.2).

Flounder ranged in length from 6.3cm to 27.5cm (Fig. 3.6). The presence of roach suggests a strong influence from freshwater on this lagoon.

Table 3.2. Number of each species captured by each gear type in Inch Lough, October 2009

Beach seine Fyke net Beam trawl Scientific name Common Name Total (0) (4) (4) Gasterosteus aculeatus Three-spined stickleback - 103 119 222 Platichthys flesus Flounder - 164 3 167 Anguilla anguilla Eel - 29 3 32 Salmo trutta Brown trout - 9 - 9 Salmo trutta Sea trout - 3 - 3 Rutilus rutilus Roach - 3 - 3 Pomatoschistus microps Common goby - - 2 2 Salmo salar Salmon - 1 - 1

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12

10

8

6

Number Number offish 4

2

0 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 Length cm

Fig. 3.6. Length frequency distribution of a sub-sample of flounder captured in Inch Lough, October 2009 (n = 73)

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4. SUMMARY

A total of 8 and 32 fish species (sea trout are included as a separate ‘variety’ of trout) were recorded in Inch Lough and the Swilly Estuary, respectively. The Swilly Estuary exhibited the highest fish species richness for any transitional water body surveyed nationwide during 2009. Juveniles of a number of commercially important fish species were present, including cod, plaice and whiting, as well as other species of angling importance, such as sea trout, flounder and lesser spotted dogfish. Species richness and distribution among all transitional water bodies surveyed during 2009 can be seen in the 2009 WFD summary report (Kelly et al ., 2010).

An essential step in the WFD monitoring process is the classification of the status of transitional waters, which in turn will assist in identifying the objectives that must be set in the individual River Basin Management Plans.

A new WFD fish classification tool, Transitional Fish Classification Index or TFCI, has been developed for the island of Ireland (Ecoregion 1) using Northern Ireland Environment Agency (NIEA) and CFB data. This is a multi-metric tool based on similar tools developed in South Africa and the UK (Harrison and Whitfield, 2004; Coates et al., 2007). The TFCI is still undergoing further development in order to make it fully WFD compliant and to account for differences in estuary typologies; however, at this stage it has been used, along with expert opinion, to provide draft ecological status classifications for each transitional water body surveyed for the WFD.

Using this approach, both the Swilly Estuary and Inch Lough have been assigned draft ecological status classifications of “Good” based on the fish populations present.

The EPA have assigned the Swilly Estuary an overall interim draft classification of “Moderate” status, based on general physico-chemical elements, phytoplankton and macroalgal growths.

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5. REFERENCES

Coates, S., Waugh A., Anwar A. and Robson M. (2007) Efficacy of a multi-metric fish index as an analysis tool for the transitional fish component of the Water Framework Directive. Marine Pollution Bulletin, 55 , 225-240.

Harrison, T.D. and Whitfield, A.K. (2004) A multi-metric index to assess the environmental condition of estuaries. Journal of Fish Biology , 65 , 683-710 ( www.blackwell-synergy.com )

Kelly, F., Harrison, A., Connor, L., Matson, R., Wightman, G., Morrissey, E., O’Callaghan, R., Feeney, R., Hanna, G., Wögerbauer, C. and Rocks, K. (2010) Sampling Fish for the Water Framework Directive – Summary Report 2009 . Central and Regional Fisheries Boards.

King, J.J., Marnell, F., Kingston, N., Rosell, R., Boylan, P., Caffrey, J.M., Fitzpatrick, Ú., Gargan, P.G., Kelly, F.L., O’ Grady, M.F., Poole, R., Roche, W.K. and Cassidy, D. (2011) Ireland Red List No. 5: Amphibians, Reptiles and Freshwater Fish . National Parks and Wildlife Service, Department of Arts, Heritage and the Gaeltacht, , Ireland.

NPWS (2003) Lough Swilly. Site synopsis, site code: 002287 . Available at: http://www.npws.ie/media/npwsie/content/images/protectedsites/sitesynopsis/SY002287.pdf

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