Seasonal changes in trophic position and food sources of deep subalpine lake (Lake Iseo, Northern Italy) zooplankton taxa were investigated during the year 2011. Furthermore, it's combined carbon and nitrogen Stable Isotope Analysis (SIA) with size-specific analyses of both, the major predatory cladoceran (Leptodora kindtii, Focke) and two potential preys (Daphnia longispina complex and Eubosmina longicornis). SIA studies have been extremely useful to track the energy flow through complex trophic network, however, if it is applied to analyze relation between two/few species may lead to misleading interpretations. In fact, integrating size-specificity allowed for understanding why L. kindtii nitrogen isotopic fingerprint fully overlapped with Daphnia, in spring. By investigating changes in L. kindtii's feeding basket, we found that in spring, L. kindtii mainly relied upon E. longicornis as prey, Daphnia being of too large body size for being captured by L. kindtii. Among preys encountered directly in front by a free-swimming Leptodora, only those able to fit into basket opening can be captured. As basket diameter increases with animal body length, size selection of prey depends on L. kindtii body length. As in other deep, subalpine lakes, E. longicornis was less 15N-enriched than Daphnia, most likely because of exploiting nitrogen fixing, cyanobacteria colonies, commonly detected in Lake Iseo with the onset of thermal stratification. Cyclopoid adults were at the top of zooplankton food chain and they could potentially be feeding on Daphnia. They, however, likely fed in a different habitat (>20 m deep water), as suggested by a rather than negligible carbon fractionation. The results overall suggest that size-specificity is crucial for addressing space and time changes in trophic links between organisms composing the two hierarchical levels within open water zooplankton community.