Marine fungi are prominent components of plankton communities, but to date little is known about how the different community members are integrated into trophic networks and whether fungal cell numbers/biomass reach a size that can be considered significant for the carbon cycling and food web chains. To shed light into this black box, we linked tag-sequencing based classification and CARD-FISH enumeration of mycoplankton communities sampled from a marine time series station in the North Sea in two successive studies and modeled fungal interactions with other plankton groups over complex weighted Topological Overlap (wTO) networks. The wTO analysis reported significant negative relationships for half of all fungal OTUs with phyto- and zooplankton groups, but also between fungi. Zoosporic fungi, including several newly identified clades, held a special position within the modeled food webs with highest numbers of connections. During the spring phytoplankton bloom, Rozellomycota zoospores reached values of 106 cells L-1 similar to what is reported for freshwater mycoloops. Furthermore, saprotrophic yeasts showed distant frequency patterns over the course of the year. At the end of the spring phytoplankton bloom, yeast cell number increased 11-fold within a week and reached biomass values with a maximum of 8.9 mg C m-3 comparable to values of filamentous fungi in the Chilean upwelling system. Our results suggest that marine mycoplankton is integrated into trophic networks over different planktonic interactions, causes trophic upgrading, and are part of the microbial loop.