Trophic interactions are central in understanding ecosystem processes and the management of natural ecosystems but are frequently complex to estimate. To address this issue, body size has been shown to be a useful trait to reconstruct species interactions, particularly in aquatic ecosystems. An allometric niche model (aNM) considering body size as a niche trait is proposed to predict trophic interactions in temperate freshwater ecosystems. The aNM calibration was based on 26 ubiquitous freshwater species with known minimal and maximum prey body sizes that permitted the establishment of prey body size ranges for vertebrate and invertebrate consumers. The aNM inferences were validated for 13 empirical freshwater food webs, and the model was applied to an extensive inventory of 474 species (spanning six orders of body size magnitude) from the largest natural French lake (Lake Bourget). This application permitted to strengthen the aNM validation with predator‐prey mass ratio comparisons, predicted diet analyses, and allowed the exploration of the lake food web structure. The aNM provided appreciable intrinsic validity (specificity = 87 ± 12%, sensitivity = 59 ± 29%, accuracy = 81 ± 10%), and departures among inferred and empirical trophic interactions were explained by foraging specificities or limited sampling of stomach contents. In Lake Bourget, 26,037 trophic links were inferred. Predator–prey mass ratios for vertebrates and invertebrates were consistent with those empirically established and were occasionally higher for invertebrates as the aNM considers small prey (e.g., bacteria) as possible resources for invertebrates. The inferred diets for three species selected for their well‐known foraging ecology also revealed plausible outcomes of the aNM. The nested structure of the lake food web was determined by highlighting different topologies among the benthic and the pelagic food sub‐webs and the role of top predator fish in the coupling of both food sub‐webs. Due to the large number of species inventories available worldwide for freshwater ecosystems anchored in the ecological monitoring, the aNM may represent a valuable tool for both ecologists and managers to address complementary facets of applied biodiversity studies (e.g., reconstruct highly resolved food webs, predict pressures on important species or new interactions with invasive species).