Aquaculture is a rapidly growing and vital industry for Scotland, with Atlantic salmon farming at its core, making it one of the country’s leading food exports. To ensure sustainable operations and minimise environmental impact, Scottish aquaculture operators are required to comply with stringent national regulations.
At Ocean Ecology, we employ advanced techniques to provide accurate and efficient monitoring at every stage, from pre-site development to the ongoing compliance monitoring of established fish farms, ensuring full compliance with the criteria set by Scotland’s governing bodies, such as the Scottish Environment Protection Agency (SEPA).
Why aquaculture monitoring matters
Monitoring aquaculture sites is essential to identifying trends in environmental conditions, minimising environmental impacts and promoting sustainable practices. Comprehensive monitoring is required both before the establishment of a new site and throughout its operational lifespan.

Baseline surveys
Marine developers proposing to build new aquaculture sites are required to undertake an initial site survey. These baseline surveys, often involve the collection of underwater imagery and video to help identify suitable seabed areas for fish farm development. The role of these surveys is to help establish whether or not proposed developments could go ahead with minimal environmental disruption while ensuring the protection of ecologically important or sensitive marine habitats.
The results of a baseline survey are submitted to environmental regulators as part of the application for a license or consent to operate. This ensures that the planned development complies with environmental protection laws and sustainable development policies.
Ocean Ecology provides expert knowledge and advice to fulfil these requirements by collecting and analysing seabed imagery to produce habitat maps and assess potential impacts of marine pen fish farms on the surrounding habitats and species with a special focus on Primary Marine Features and their sensitivity and recovery potential from any impact.
Benthic compliance
Benthic compliance monitoring is a critical component of sustainable aquaculture. In Scotland, SEPA enforces regulations to limit environmental impacts from operational fish farms. Areas immediately surrounding fish pens can experience organic waste accumulation, including uneaten feed and fish excreta, which decompose and reduce oxygen levels, potentially making the seabed uninhabitable for many organisms.
To mitigate these effects, operators must manage sites responsibly to avoid significant harm to seabed biodiversity beyond permitted boundaries. Aquaculture facilities are typically sited away from areas known to be sensitive and are subject to regular benthic compliance monitoring to ensure that the effects of organic enrichment remain within acceptable limits.
Sustainable aquaculture begins with responsible monitoring. By taking a thorough, multi-faceted approach both before and during site operations, we help ensure long-term environmental protection, providing clear, evidence-based advice and robust data to aquaculture companies, supporting their efforts to maintain high standards and meet the requirements of regulatory bodies.

Infaunal Quality Index
Advanced tools and matrices, such as the Infaunal Quality Index (IQI), help us to analyse the infaunal community and environmental parameters around an aquaculture site to determine environmental conditions. This enables a more accurate assessment of benthic ecosystem health for sustainable aquaculture management.
The IQI is used to assess the ecological status of macrobenthic infaunal samples and is based on a weighted average of three biological metrics:
- Taxa richness: number of taxon groups when identified to lowest taxonomic level
- AMBI score: a weighted sensitivity score of all individuals within the sample. AMBI scoring was developed to explore the response of soft-bottom communities to anthropogenic changes in water quality. The AMBI group system contains five groupings with sensitive species being categorised as I and more tolerant and pollution indicating species classified as an AMBI group V.
- Simpson’s evenness: a measure of the distribution of the individuals across the different taxonomic groups

Our capabilities and experience in the Finfish Aquaculture Sector are not limited to baseline and compliance monitoring. We also work with clients to develop sampling strategies, undertake sampling and analyse data to compile a comprehensive and detailed assessment of the environment surrounding aquaculture sites.
We have also undertaken and continue to work on aquaculture site characterisation, including ADCP current measurements, discharge assessments, SLICE monitoring and the provision of expert fish health services.
To find out how our our monitoring programmes can ensure your aquaculture project meet compliance regulations, contact us now



















