Aquatic microbial food webs are in general size structured. Phytoplankton, which constitute the base of the food web, are grazed by protozoa and mesozooplankton, which in turn are consumed by planktivorous fish. Food web efficiency (FWE) is a measure of how efficiently energy is transported up the food web. FWE is low if the phytoplankton is inedible by the grazers, while FWE is higher if the phytoplankton community is dominated by edible phytoplankton. Recently, the presence of microfungi in aquatic food webs have been suggested to facilitate energy transfer up the food web, via the “mycoloop”. The aim of the study was to set-up a model system of phytoplankton – zooplankton food chains, relevant to the Baltic Sea, and to test FWE in diatom and flagellate-based food webs. Further, I wanted to introduce microfungi in the system and observe their impact on FWE. After many phytoplankton and zooplankton species tests, I decided to perform grazing experiments using one grazer, the ciliate Tetrahymena pyriformis, and two phytoplankton species: a diatom (Skeletonema marinoi) and a flagellate (Rhodomonas baltica). I hypothesized that T. pyriformis would more efficiently feed on flagellates than on diatoms. I performed a grazing experiment where the increase in ciliate abundance was measured, the consumption of the phytoplankton monitored and the FWE estimated. The diatom-based food web led to 14 times higher FWE than the flagellate-based food web. The variation in FWE may be explained by a difference in initial abundances introduced in the experimental treatment, which created unequal grazer:prey ratio between treatments. Further, the swimming behaviour of the flagellate might have reduced the capture efficiency by the ciliate. Microfungi were introduce in an experiment, from a natural seawater sample, but fungal infection was not observed for any of the tested phytoplankton species. Further development is needed to test the effects of microfungi on marine FWE.