Mediterranean ponds are shallow water bodies and often temporary. In the past, they were important sources of water, and recently are exposed to various negative anthropogenic impacts. Zooplankton organisms contribute significantly to pond biodiversity and are relevant indicators of ecological status. The objectives of this study were to establish: (i) the abundance and diversity of zooplankton and the ecological role of dominant species; (ii) the influence of environmental factors and predation on zooplankton composition; and (iii) the correlation of zooplankton functional traits and ecological status as basis for the proposal of management and conservation of Adriatic ponds. Among 57 zooplankton species, rotifers dominated with 40 species. The results indicate the zooplankton composition was significantly influenced by complexity of the macrophytes and fish predation. Zooplankton in ponds with submerged macrophytes, without fish, were characterized by high abundance and diversity in very good ecological status and higher ratio of planktonic crustaceans. In ponds of good ecological status with dominance of rotifers, fish were present, and coverage of emergent and flotant macrophytes. The low abundance and diversity of zooplankton marked ponds of moderately altered ecological status with scarce macrophyte coverage. Anthropogenic impacts on Mediterranean ponds require systematic management and conservation to minimize adverse impacts and restore their ecological functions and preserve biodiversity.