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In aquatic ecosystems, young of the year (YOY) fish often exhibit strong interannual fluctuations. Because these fish prey on zooplankton and are preyed upon by piscivorous fish, strong fluctuations in their abundance may have important impacts on food web functioning. The static Ecopath model was used to assess potential impacts of strong fluctuations in YOY perch in the deep peri-alpine Lake Annecy. We modeled two contrasting years in terms of YOY perch biomass: a situation with a high biomass of YOY perch and a situation with a low biomass of YOY perch. Additionally, five models were derived from the two initial models to better explore the effects of YOY perch biomass fluctuations on food web functioning. Disparities were revealed in terms of the activity of the system (volume of flows) and the trophic transfer efficiency. When the YOY perch biomass was high, the volume of flows within the system was less important, but the trophic transfers were more efficient than when the biomass was low. The high biomass of YOY perch appeared to facilitate transfers from low to high trophic levels. The results indicated that strong variabilities in the abundance of YOY fish had little impact on the main food web flows and pathways because of the capacity of predators to feed on various prey (omnivory) but could induce significant differences in food web properties (e.g. ascendancy, robustness) and organization (e.g. cycling, mean trophic level).