The South Pacific freshwater ecosystems have never been investigated systematically. Although their ecological value has long been recognized and recommended for protection, little action has been taken so far. Here, we present results of 39 lentic water bodies on 18 islands belonging to seven countries. Temperature, conductivity, and pH were measured and samples of aquatic organisms were collected. Freshwater algae, nematodes, rotifers, ostracods, copepods, cladocerans, and aquatic oribatid mites were identified to genus or species level. Sixty-six percent of all taxa recorded have a cosmopolitan distribution, 14% are circumtropical/tropicopolitan species, and for 20% a restricted distribution predominantly in Australasia has previously been reported. Eleven new copepod and three new ostracod taxa were discovered. Out of 39 water bodies we found at least 17 stocked with nonindigenous fish species. Salinization and uncontrolled introduction of alien fish species may lead to reduced species richness in these remote freshwater ecosystems. The highest species richness was recorded in old, shallow, fish-free softwater lakes at high altitude.