Zooplankton organisms occupy a central role in the food webs of shallow water bodies, and are known indicators of ecological changes based on their structural (diversity, abundance, biomass) and functional (feeding) traits. Shallow lakes of temperate-continental and Mediterranean climates differ related to the effects of environmental factors, which cause differences in the interactions of abiotic and biotic factors. The aim of this study was to determine: (i) the diversity, abundance and trophic structure of zooplankton; (ii) zooplankton indices in comparison to the trophy state indices; (iii) a proposal for measures in the management and conservation of shallow water bodies in two different climates of Croatia. In nine ponds, 48 species of zooplankton were determined, and rotifers dominated with 36 species. Habitat complexity, macrophyte coverage, and nutrient concentrations were indicated as significant factors in the structuring of zooplankton in shallow water bodies of both geoclimate regions. Zooplankton in the temperate-continental climate was characterized by populations of higher diversity, while in the Mediterranean climate zooplankton was characterized by populations of higher abundance, particularly species of genera Lecane and Brachionus. Results of this study support the importance of zooplankton as a sentinel indicator in assessing the trophic and ecological status of shallow water bodies and provide a basis for determining guidelines in the conservation and management of these sensitive and endangered ecosystems.