This study investigates the adaptation of certain feeding strategies by a population of Atherina boyeri inhabiting a freshwater ecosystem (Lake Trichonis, Greece) and links feeding habits with ecosystem interactions, using stomach content analysis and food availability. The use of Ivlev's electivity index (E) revealed the selection of different prey categories in respect to size, species and even gender. A. boyeri showed positive selection for larger zooplankters such as adult copepods and the egg-bearing females of Eudiaptomus drieschi (0.53 < E < 0.92 and 0.24 < E < 0.99, respectively) or the cladocerans Diaphanosoma orghidani and Daphnia cucullata (0.25 < E < 0.53 and 0.23 < E < 0.37, respectively) in spring and/or summer. In contrast, the fish totally avoided rotifers and copepod nauplii, while showing negative selection for smaller prey items like copepodites (−1.00 < E < −0.14). A shift to larger prey was recorded as age increased. Larger specimens showed cannibalistic behaviour by consuming larvae of A. boyeri and the endemic, threatened, fish Economidichthys trichonis. The results provide certain indications that, through selective predation, A. boyeri is able to affect zooplankton abundance and community composition, the vertical distribution and migration of crustaceans and the abundance of other fish species, However, more research on the dynamics and feeding ecology of A. boyeri and other fish species is necessary.