Abstract Wild and farmed mussels, Mytilus edulis, coexist with salmon farms in Scottish sea lochs. A synthetic pyrethroid, cypermethrin, is licensed for use on fish farms to control sea lice infestations as a formulation called Excis®. In this study, uptake of cypermethrin from Excis® exposure is investigated through the use of gas chromatography with mass-spectrometry. The effects of Excis® on mussels are also examined by measuring the neutral red retention time of lysosomes, aerial survival and shell closure. The isomeric ratios of cis:trans cypermethrin measured in mussels are around 80:20; a marked increase from 40:60 to which the mussels were exposed. This is most likely due to preferential metabolism of trans-isomers, as the same response is seen in vertebrates. There is a pronounced behavioural effect of shell closure, where mussels exposed to 1000 μg/l cypermethrin shut their shells within an hour of exposure. Arguments are presented for this effect being either a voluntary response on recognition of cypermethrin, or an effect arising from an involuntary action of cypermethrin on the adductor muscle. Even at 1000 μg/l cypermethrin, neutral red retention time and aerial survival are not affected. The data suggest that the responses of mussels shown here are unlikely to occur in the field, even at the concentrations of cypermethrin used in fish cages, for the treatment of sea lice.