A multivariate analysis of juvenile fish community data, sampled at two nursery sites at an interval of 17 years (2000—early, and 2017—late), was conducted to elucidate the trends of change in littoral juvenile fish communities along the eastern Adriatic coast. Fishing, trophic and taxonomic composition to the community data were analysed for possible causality. The ichthyofaunal composition differed significantly for Site, Period and all interactions. According to the mMDS ordination plot, four groups of communities were defined, with clear cyclicity. No patterns were found in species composition between sites in the early period, while the observed community changes were governed by the same pattern at both sites in the late period. The species that contributed most to the observed changes were non-commercial, small, benthic resident fishes, such as gobiids and blennids, or those associated with canopy alga for shelter and feeding. The analysis correctly allocated samples based on community information to Sites and Periods. The data obtained provided an invaluable opportunity to test for the generality of potential patterns of change in littoral fish communities, suggesting that significantly modified juvenile fish communities may be the result of constant human embankment and marine infrastructure construction along the coast in recent decades, rather than climate change or fishing pressure, as generally considered.