The physical and biochemical properties of Atlantic cod (Gadus morhua) wastes were analysed, and the waste remediation potential of blue mussels (Mytilus edulis) was assessed. Waste generated daily by Atlantic cod represented 24.9% of the cod feed added to the system. Particle distributions determined using a Coulter Multisizer and image analysis revealed that the majority of the particles in terms of numbers occupy the smaller size ranges; however, larger particles occupy a larger proportion of the volume. Effluent was composed of particles <70 μm (36%), 70–500 μm (31%) and particles >500 μm (33%) by weight. The amount of dissolved carbon and nitrogen associated with the effluent represented 3.1% and 3.7%, respectively, of the total feed added to the system daily. Particles <70 μm had significantly less organic matter, lipids and fatty acids and were expected to be ingested more by mussels than larger particles. The major lipid classes present in effluent were free fatty acids, triacylglycerols, phospholipids, acetone mobile polar lipids and sterol. Cod effluent contained two essential fatty acids DHA and EPA, a diatom marker (16:1ω7), as well as two zooplankton markers 22:1ω11 and 20:1ω9, which accumulated in mussels and may serve as markers for aquaculture wastes. Although only 36% of the effluent was of a size suitable for mussel ingestion, this size fraction has the greatest potential to spread to surrounding areas. These particulates may be useful as an alternate food source when natural seston is low.