Greece is situated in the East Mediterranean region and in the Balkan peninsula, i.e., a European biodiversity hotspot with high endemism in subterranean and freshwater fauna, highlighting the need to understand its biodiversity. A literature search was undertaken to present a checklist of cladocerans and copepods based on a compilation of published and current data, from 1892 up to 2022 from inland surfaces and subterranean water bodies from different regions of Greece. For Cladocera, 80 species were recorded (9 families with 35 genera). The most diverse families were Chydoridae (20 genera with 33 species) and Daphniidae (5 genera with 27 species). For copepoda, 134 taxa were recorded, in surface water bodies (12 families with 34 genera), subterranean water bodies (7 families with 27 genera), and parasitic copepods (3 families with 3 genera). The most diverse families in surface waters were Cyclopidae (15 genera with 41 taxa) and Diaptomidae (5 genera with 17 species), while those in subterranean waters were Cyclopidae (11 genera with 35 taxa) and Canthocamptidae (6 genera with 17 taxa). More species are expected to be discovered after sampling understudied regions, especially islands, as well as water bodies such as temporary pools, swamps, ditches, puddles, and the littoral parts of lakes, while molecular studies are needed to clarify various cases of complex taxonomy.