All organic matter, fatty acids (FA) in particular, is transformed in the pelagic plankton food web before reaching fishes or benthic organisms. Mesozooplankton (0.2 to 2 mm) is the main conduit for FA transfer, and FA profiles in sedimenting matter should therefore be significantly affected by its activity. To test this hypothesis, we sampled seston, zooplankton and sediment trap material for FA analysis during 5 campaigns spanning 4 seasons at a coastal site on the west coast of Sweden. Saturated (SAFAs) and monounsaturated (MUFAs) FAs dominated seston and trap material, while copepods contained 75 to 90% polyunsaturated FAs (PUFAs). Sedimentation of bulk particulate organic carbon did not vary significantly with season (coefficient of variation, CV = 33%), while pigment (CV = 49%) and in particular faecal pellet fluxes (CV = 100%) were highly variable as a result of copepod feeding activity. Copepod feeding, pellet production and egg production were all high after the spring bloom and in summer and autumn. Overall, 5 to 25% of the sedimenting FAs were affected by copepod feeding activities, and the supply of PUFAs to the benthos was significantly enhanced by copepod grazing activity. SAFAs and MUFAs were enriched by 5 to 10% in sediment traps, while the proportion of the most important PUFA, docosahexaenoic acid, was reduced by up to 15% in summer and autumn. In conclusion, the periods of significant input of PUFAs to the sediment coincide with the period of highest transformation by the mesozooplankton, which in the present study was summer and autumn.