The amphipod, Echinogammarus marinus, is common in sheltered coastal inlets, such as estuaries and sea lochs, in Scotland and exhibits increased levels of intersex in some contaminated areas. Sea lochs are commonly the location for coastal aquaculture development, and some chemicals used in fish-farming are specifically designed to target the crustacean nervous system. Therefore it was hypothesised that these chemicals may also affect neuro-endocrine pathways, causing morphological and reproductive abnormalities in non-target Crustacea. Based upon this hypothesis, Echinogammarus marinus amphipods from two different Scottish sea lochs containing salmon farms were investigated. Morphology, intersexuality, and the incidence of microsporidian parasites were recorded at sites close and at distance from fish-farms. Results suggest a higher incidence of intersexuality at sites within sea lochs, comparable to that observed in industrially contaminated sites elsewhere in Scotland. The data suggest that fish farming activity may influence the observed distributions of intersexuality within lochs. Intersex specimens were more likely to be infected by microsporidian parasites than non-intersex specimens. Normal females were found more likely to be infected by microsporidian parasites at sites associated with high intersexuality, suggesting the parasite as the probable feminiser. The cause(s) for the observed patterns of intersexuality are unclear, although suggestions relating to discharges from fish farms are discussed.