At temperate latitudes where seasonal changing environmental conditions strongly affect the magnitude, duration and species composition of pelagic primary production, macrobenthic organisms living below the photic zone rely on the sedimentation of organic matter as their primary energy source. The succession from nutritious spring blooms to summer cyanobacteria is assumed to reduce food quality for benthic primary consumers and their fatty acid (FA) profiles. In contrast, we find low seasonal variability in FA content of five benthic macroinvertebrates spanning two trophic levels in the Baltic Sea, a system with high seasonal variation in phytoplankton species composition. However, levels of the major FA groups vary greatly between benthic species. The results suggest that benthic macroinvertebrates have evolved FA metabolism adapted to degraded sedimenting material. Moreover, our study shows that species composition of benthic macrofauna rather than seasonal changing conditions affect availability of essential nutrients to higher trophic levels.