Changing abiotic factors, like temperature and light are important drivers of seasonality, affecting aquatic ecosystems and organisms annually in a predictable pattern, structuring species composition, growth, reproduction and trophic interactions. As a consequence of human induced climate change, coastal ecosystems are seeing a disruption in the predictability of annual cycles. This in turn is affecting species composition at the base of the food web, possibly causing effects for higher trophic levels. Although the benthic and pelagic environments are coupled, still very little is known about the effect that changes in species composition will have on this interaction. In Study I, three species of common macrofauna from Baltic Sea soft sediment bottoms were for the first time subjected to a gradient of spring bloom related diatoms and summer bloom related cyanobacteria as food resource. We found a clear differentiation between the two food types regarding preference of the consumers. The results highlight that diatoms were consumed by all species with a strongly positive linear relationship with available food. Cyanobacteria was consumed, but with no clear pattern relating to amount available. In Study II, we investigated if seasonal phytoplankton succession affects the composition of essential compounds in benthic macrofauna, focusing on transfer of fatty acids (FAs) from phytoplankton via sediment to benthic consumers. The outcome showed for the first time large interspecific variation in FA composition and concentration, but low seasonal variation within species for five major invertebrate taxa over three seasons. We found only few convincing links between seasonal phytoplankton production and its succession of FAs in the seston, sediment and the animals. This suggests that demands for FAs differ substantially between taxa and that FAs of sedimenting organic material is not clearly reflected in the investigated species. In Study III, we quantified recruitment of phyto- and zooplankton from oxic sediment to the pelagic environment, under proposed changes to light and temperature caused by climate change. We found clear indications of both light and temperature having an effect on phytoplankton (mainly cyanobacteria and dinoflagellates) recruitment in spring. We found no effect on recruitment of phyto- or zooplankton in summer, but large differences in zooplankton recruitment in summer compared to spring. The phytoplankton taxa that showed strong recruitment responses in spring, could with proposed climate change scenarios potentially impact the species composition during spring, thus affecting food web dynamics. In Study IV we used advanced molecular tracing techniques of compound specific stable isotope analysis of carbon and nitrogen in amino acids in five taxonomic groups of phytoplankton, with the goal to advance methods of differentiating between groups in mixed samples of phytoplankton. By applying this method to amino acids, we were able to differentiate between all five taxonomical groups. The key in revealing the group specific finger printing on particular amino acids was based on amino acid synthesis pathways and thus depletion or enrichment of isotopes. The novel findings presented in this thesis further advances our knowledge about responses of benthic-pelagic coupling to environmental change and how to further develop tracing of food webs in order to predict the effects of a changing environment on aquatic organisms.