Recent investigations of molecular diversity in the plankton of lakes and coastal lagoons have detected an unexpected diversity of fungi including chytrids. Microscopic observations have provided evidence for the presence of two main forms. The sporangia are implied in algal parasitism. The propagules, i.e. uniflagellated zoospores, may constitute an alternate resource for consumers. These results suggest a need to reconsider the concept of plankton food web functioning. In order to describe the potential role of fungi in food web functioning, we revisit the model of carbon flows in the photic zone of the North basin of Lake Biwa in summer, established using the inverse analysis method for estimating missing flow values. In the absence of quantification of the flows induced by fungal activity, simulations are realised of their potential role in the plankton food web. Different rates of parasitism of micro-phytoplankton are tested, with a return of this carbon to the consumer via the consumption of zoospores by mesozooplankton and, at a lower rate, microzooplankton. The presence of this indirect pathway channelling micro-phytoplankton production to the consumers via the fungi, leads to the following trends: (i) an enhancement of the trophic efficiency index, (ii) a decrease of the ratio detritivory/herbivory, (iii) a decrease of the percentage of carbon flowing in cyclic pathways, and (iv) an increase in the relative ascendency of the system. Relative ascendency, which indicates pathways more specialised and less redundant, is related to theories linking food web patterns and stability. A high ascendency in the plankton food web (low trophic level), if connected to a food web of high redundancy at higher trophic levels (e.g. nekton food web) would fit well to the stabilising pattern called structural asymmetry, considered a stability criterion. More precise models, taking into account the species diversity of fungi and the high specificity of their parasitism on the micro-phytoplankton, would further accentuate this observation.