Information on fish and fish habitat

SEPA will require information on how important the watercourses involved are to fish and fisheries at a local, regional, catchment, national or international level, and details including the locations of the present upstream limit(s) of salmon, sea trout, eels, lamprey, spawning river trout or loch trout (this list may include other species at certain sites) in the watercourses or, as appropriate, downstream of them. Your local District Salmon Fishery Board or Fisheries Trust may be a helpful start.
We will require an assessment of the suitability for fish in the river habitat between the upstream end of the impounded river flow and the scheme outfall and further upstream if it is possible that spawning fish can ascend all the way up the stretch between the outfall and the intake to access habitat upstream. The level of detail required will depend on the relative risk of the scheme, as outlined in the fish survey information requirements in the table below.
SEPA will require applicants to identify likely natural and artificial obstacles to fish migration upstream and downstream of the intake structure. This is because watercourses which are accessible to migratory fish often contain a more diverse and abundant fish community than areas not accessible to migratory fish above high waterfalls, and additional mitigation may be required in these cases. Annex B describes the information required on obstacles to migration. Where there is uncertainty over the significance of a waterfall, we may require the applicant to provide fish survey data to assess in more detail whether it is an impassable obstacle for all species. It is very important that the exact location of any waterfall which is suggested to be impassable is given, and that the justification for considering it to be impassable is given.
In certain cases, we will also require information on fish populations. The information required and the circumstances in which it is needed are summarised in the following table. Part 3 of Annex B explains how to collect, as applicable, quantitative or semi-quantitative information on fish populations.

Table 4: Fish survey information requirements

Distance measured along the middle of the river channel between the upstream limit of impounded river flow and the outfall (metres)

River width (metres)
<1 1 to <2 2 to 5 >5
20 to <100 N, HP N, HP N1, HP S, HP
100 to <250 N, HP S, HP S, HP S, HP
250 to <500 N, HP S, HP Q, HP Q, HF
≥500 S, HP Q, HF Q, HF Q, HF


1 See note below concerning Special Areas of Conservation:  

No survey is required if:  

  • the distance measured along the middle of the river channel between the upstream limit of impounded river flow and the outfall is less than 20 metres;
  • the river bed is entirely, or almost entirely, smooth bedrock of a character which provides no cover for fish;
  • the river bed is entirely artificial (eg a concrete bed);
  • the entire scheme is to be located above an obvious natural obstacle* to migration of salmon, sea trout, lampreys and eels or river or loch trout and the habitat does not contain fish populations which are known to be rare or distinct  (clarification from SEPA and SNH should be sought on this last point if necessary –such a river will generally contain a population of resident brown trout);
  • SEPA already holds the relevant information – please check with SEPA before undertaking any survey work.  

*In all cases where likely obstacles to fish migration are identified, photographs of the obstacles should be provided, including a reference object to allow the scale of the obstacle to be judged. Photographs should be taken at a range of water flows to allow the obstacle to be assessed accurately.  

If it is possible that spawning fish can ascend all the way up the stretch between the outfall and the intake to access habitat upstream, survey work upstream may also be required and this should be discussed with SEPA.  

N: No fish habitat survey and no electrofishing survey required.  

S: Semi-quantitative electrofishing survey.  

Q: Quantitative electrofishing survey.  

HP: Qualitative habitat survey comprising photographs of the affected stretch showing characteristics of the bed and banks and significant obstacles to migrating fish species. The photographs should be taken at times of low flow and sufficient water clarity so that the composition of the bed can be clearly seen. Measurements of the width and depth of the river channel, and the location at which they were measured, should be attached to each photograph.  

HF: Full fish habitat survey as described in Part 1 of Annex B.  

If a river falls into a category where no survey is required, assumptions will be made by SEPA about what fish it is most likely to contain.  

Where the river is within, or connected to, a Special Area of Conservation (SAC) for Atlantic salmon or freshwater pearl mussel, a qualitative habitat survey will be required in support of applications that otherwise would require no fish habitat survey or electrofishing survey. A semi-quantitative electrofishing survey will also be required if the river is 2 to 5 metres wide and the affected length less than 100 metres. Further survey information may also be required in SACs in particular circumstances, and in such circumstances applicants are strongly encouraged to have early discussions with SEPA and SNH.