The purpose of this study was to determine biochemical changes occurring in blue mussels (Mytilus edulis) fed effluent from an Atlantic cod (Gadus morhua) aquaculture facility over a period of ten weeks, compared to those in mussels fed a commercial shellfish diet and those supplied only filtered seawater. The total lipid and fatty acid content (mg g-1 wet weight) significantly decreased for mussels fed effluent during the experiment. The only change in the lipid class composition (% total lipid) at the end of the experiment was a significant increase in the proportion of acetone mobile polar lipids. There were several significant changes in the fatty acid composition (% total fatty acid) including an increase in the proportion of 18:1ω9, 18:2ω6, 20:4ω6, 21:5ω3 and the dienoic non-methylene-interrupted fatty acids 20:2a and 22:2b and significant decreases in the proportions of 16:0, 18:4ω3 and 20:5ω3. The increase in non-methylene interrupted dienes suggests that the amount of essential fatty acids in the effluent may be insufficient for optimal mussel growth. The presence of the terrestrial plant marker 18:2ω6 in both the fish feed and the effluent and its increased proportion in mussels fed effluent suggest that this fatty acid may have potential as a marker for aquaculture wastes.