Inshore fish (estuaries and reduced salinity sea lochs)

Transitional water processes are driven by variations of freshwater influx, tidal movements and sedimentation. The TFCI responds to anthropogenic pressures such as port activities, dredging, reclamation, cooling water abstraction, and pollution from urban, industry, agriculture and aquaculture. The TFCI was developed for WFD classification using fishes as an indicator of the quality status of transitional waters (Coates et al., 2004, 2007, UKTAG, 2014). The TFCI considers four community characteristics that are represented by ten separate metrics (Table a).

Using monitoring data, each metric is assessed or scored according to the degree of departure from a reference condition; these scores are then combined into a single, integrated multi-metric index. All metrics have equal weighting in terms of their contribution to the overall result. To meet the requirements of the WFD, the final index values are re-scaled to give an Ecological Quality Ratio (EQR), which ranges between 0 and 1. The EQR is divided into five class bands: High, Good, Moderate, Poor, and Bad which depend upon the level of impact on the fish community (Table b).

The development of the TFCI followed a multi-metric approach, which has been successfully applied to transitional waters (estuaries) both globally and in Europe in the context of the WFD (e.g. Miller et al., 1988; Deegan et al., 1997; Gibson et al., 2000; Hughes et al., 2002; Borja et al., 2004; Harrison & Whitfield, 2004; 2006; Breine et al., 2007; Coates et al., 2007).

The selection of metrics was devised following a review of existing estuarine multi-metric fish indices and further discussion by the UK Fish Task Team (Coates et al., 2004). The candidate metrics are based upon either presence/absence data, relative (%) abundance data or number of taxa present. A full description of the metrics and development of the TFCI can be found in Coates et al., 2007.

The use of appropriate reference conditions (in tables below) is essential for a meaningful WFD assessment of the fish community as they provide the baseline against which fish metrics can be evaluated. Reference conditions must take into account zoogeographic differences, the inherent morphological variation between transitional water types and sampling methodologies.

Two ecoregions for European transitional and coastal waters are recognised under WFD with the UK: Atlantic Ocean and North Sea. In terms of morphology, the WFD requires that transitional waters are also assigned to a typology using factors such as ecoregion, salinity, tidal range, depth, current velocity, wave exposure, residence time, water temperature, mixing characteristics, turbidity, substratum composition and shape. The purpose of assigning transitional waters to a physical type is to enable the establishment of appropriate reference conditions and to make a valid assessment of the ecological status of each system. The UK Technical Advisory Group (UKTAG) for WFD identified six types of transitional water within the UK and Republic of Ireland based on mixing characteristics, salinity, mean tidal range, wave exposure, depth and substratum (Table c).

There are four transitional waters body types present in Scotland; types TW2, TW3, TW5 and TW6. Transitional water lagoons, type TW6, are widespread but are generally inaccessible to fish and are excluded from WFD assessments for fish. Of the others, on the east coast (North Sea Ecoregion) only type TW2 occurs. On the west coast (Atlantic Ecoregion) types TW2, TW3, and TW5 are present.

Reference conditions and metric scoring thresholds for the TFCI use a combination of historical records, best available data, and expert judgement. Metric reference conditions for each region /water body type are needed to ensure an effective classification.

Reference conditions have been developed for Scottish west coast TW2 (Tables d & e) and TW5 (Tables f & g) using a combination of Scottish historical records, and recent data from Scotland and (for TW2) data from Northern Ireland which is geographically similar. The Scottish west coast data are dominated by records from the Clyde Estuary, which includes large relatively deep water areas which skews the number of reference species upwards (compared to Northern Ireland) and includes northerly species (e.g. Zoarces viviparus) which are scarcer in Ireland (or western England). Augmentation of the Scottish west coast TW2 data with additional records from the adjacent area of Northern Ireland helps diminish the bias towards the Clyde Estuary but maintains the northerly focus of the data.

Reference conditions for Scottish east  coast TW2 estuaries have been developed using Scottish historical records combined with recent data from east Scotland and an adjacent area of North East England, which is geographically similar (Tables h & i). The inclusion of TW2 data from North East England helps reduce a potential bias towards Forth Estuary records. Scottish TW3 transitional waters are restricted to the Solway Estuary and a few nearby smaller estuaries on the coast of Dumfries and Galloway. Development of specific Scottish reference conditions for TW3 has not been completed due to paucity of data and monitoring of Scottish TW3 waters is not carried out.

There are numerous pressures on transitional water (and inshore) fish communities but as detailed pressure data are not available for most areas it is it is difficult to directly relate pressures to TFCI assessment results or use pressure data as proxy assessments.

The pressures on transitional and inshore fish communities include:

• Barriers to mobile species movement e.g. for migratory salmonids, lampreys, eels);
• De-oxygenation e.g., salmonid mortalities due to summer oxygen sags in upper estuaries during warm weather and low flows, or mass mortalities of sandeels in shallow inshore bays due to localised plankton blooms;
• Emergent regime changes e.g. mortalities from power station cooling water abstraction;
• Genetic modification & translocation of indigenous species e.g., impact of accidental release of farmed salmonids on wild salmon populations;
• Introduction or spread of non-indigenous species & translocations e.g., competition of Pacific-type/red salmon entering estuaries and rivers in North East Scotland;
• Water quality;
• Organic enrichment;
• Physical change to another seabed type e.g., via dredge disposal;
• Physical removal extraction of substratum, dredging, land reclamation;
• Removal of non-target species (lethal);
• Removal of target species e.g., plaice, dab, sole removed inshore or elsewhere - impacts juvenile populations inshore;
• Siltation changes;
• Sub-surface abrasion/penetration;
• Synthetic compound contamination e.g. pesticides, antifoulants, pharmaceuticals;
• Temperature changes e.g. localised power stations thermal discharges;
• Underwater noise e.g. piling noise disruption to migrating salmonids in industrialised estuaries.

Inshore fish in transitional waters comprise species with different roles in the community such as residents, migrants passing upstream or downstream, seasonal visitors, or species using estuaries as a nursery. Each of these groups is exposed in different ways to anthropogenic pressures. Waste disposal such as sewerage discharges may cause organic enrichment and consequently reduce oxygen levels (via biological oxygen demand) in upper estuarine waters, especially during summer periods with warmer waters and lower flows. This inhibits the passage of migratory fish or causes fish mortalities. Similarly, localised enrichment may contribute to plankton blooms in shallow coastal waters causing mass mortalities of fish such as sandeels. Industrial discharges with toxic compounds (heavy metals, pesticides, anti-foulants, and pharmaceuticals) may induce sub-lethal stress in many fish species. Dredging activities, whether abstraction or disposal, or beach replenishment activities, may impact benthic species via smothering or loss of their food resource of benthic invertebrates. Inshore fishing activities remove both target and non-target fish species and impact the seabed invertebrate communities on which demersal fish feed. Energy production can have a significant impact on inshore fish communities where cooling water abstraction may remove large numbers of small or juvenile fish. Cooling water discharges may elevate local temperatures with consequent oxygen reductions. Infrastructure in the form of embankments and land reclamation may result in significant habitat loss for shallow water fish species and alter local water flow characteristics. Aquaculture poses a potential pressure on inshore fish communities via the escape of modified strains of fish, or the elevation of levels of sea lice from caged fish, both of which may then affect wild populations. The recent arrival of the non-native Pacific pink salmon in Scottish inshore waters also represents a potential threat to the native Atlantic salmon populations.

The transitional water fish communities in industrialised estuaries, such as the Clyde or Forth, may be subject to cumulative pressures acting on the habitat or species. However, direct evidence of the impact of specific pressures is difficult to determine. The transitional waters where this assessment is undertaken are highly dynamic areas and it is unknown how the different pressures cumulate and affect the species being assessed. Moreover, although the WFD method is a semi quantitative standardised assessment method of the fish community within specific transitional waters, many of the fish are not permanent residents of the water body. The fish community comprises different functional guilds – some are residents but others are seasonal visitors only, or use the inshore waters as nursery ground and move offshore as adults, and some (e.g. salmonids, lampreys, eels) undertake extensive migrations, spending only a short part of their lives inshore. These latter fish guilds may be subject to significant trans boundary pressures out with the inshore area. Although the overall multi-metric assessment tool does not highlight trans boundary impacts, they may be indicated by looking at those metrics which are related to the functional guilds. Although this assessment method could theoretically pick up rare or occasional visitors to the transitional waters (if their presence coincided with the sampling times), this is unlikely in practice as sampling frequency is limited. Sampling of some groups e.g. migratory lampreys and eels (as elvers) is probably under-represented as they migrate in spring whilst WFD sampling is focussed in autumn. Sampling intensity is probably too low to find aliens, such as the Pacific salmon, and different approaches are needed to properly assess these.