Two differently structured food webs can be distinguished in the pelagic habitat of aquatic systems; the classical one (autotrophic) with phytoplankton as a base and the microbial food web (heterotrophic) with bacteria as a base. Energy (produced at the basal trophic level) reaches higher trophic levels, i.e. zooplankton, directly in the classical food web in contrast to the microbial food web where it passes through additional trophic levels before reaching zooplankton. Energy is lost between each trophic level and therefore less energy should reach higher trophic levels in the microbial food web than in the classical food web. However, factors such as edibility of prey, temperature and properties of the predator, might also influence the food web structures and functions. In this thesis I studied which factors are important for an efficient carbon transfer and how a potential climate change might alter the food web efficiency in pelagic and pelagic-benthic food webs in the Baltic Sea. Furthermore, one of the most dominant zooplankton in the northern Baltic Sea, Limnocalanus macrurus, was studied in order to establish the seasonal pattern of lipid reserves in relation to food consumption. My studies showed that the carbon transfer efficiency during summer was not directly connected to the basal production, but factors such as the ratio between heterotrophs and autotrophs, the relationship between cladocerans and calanoid copepods and the size and community structure of both phytoplankton and zooplankton were important for the carbon transfer efficiency. In a climate change perspective, the temperature as well as the relative importance of the microbial food web is likely to increase. A temperature increase may have a positive effect on the pelagic food web efficiency, whereas increasing heterotrophy will have a negative effect on the pelagic and pelagic-benthic food web efficiency, reduce the fatty acid content of zooplankton and reduce the individual weight of both zooplankton and the benthic amphipod Monoporeia affinis. During the seasonal study on the calanoid copepod L. macrurus, I found that this species is mainly a carnivore, feeding on mesozooplankton during most of the year but switches to feeding on phytoplankton when these are abundant. Furthermore, when food is scarce, it utilizes lipids that are built up during the course of the year. From these studies I can draw some major conclusions; there are many factors that influence how efficient carbon is transferred in the food web and different factors are probably of various importance in different areas. In order to determine the carbon transfer efficiency, the various strategies exerted by different organism groups have to be considered, as for example that some zooplankton utilize lipid reserves instead of feeding all year around. Also, in a climate change perspective, the pelagic-benthic food web efficiency will decrease, as will the quality of zooplankton and M. affinis, possibly having implications for higher trophic levels such as fish.