The lakes of Chiloé Island have a high dissolved organic carbon concentration (known as “humic”) and show a connection with brackish water. They also display a high species richness of crustacean zooplankton. The aim of the present study is to characterize the potential factors that explain crustacean species richness in Chiloé Island lakes. To that purpose parameters of the abiotic environment were determined. The results of PCA performed on those data revealed the existence of three lakes with high crustacean species richness that are relatively deep, show high nitrogen concentrations, and are located at relatively high altitude. In contrast, there are two lakes with low species richness, high mineral concentration, and situated at low altitude. One of these lowland lakes gives rise to a river effluent to the sea, and it is connected to the other lake; these observations agree with the results of a performed cluster analysis. Nevertheless, the co-occurrence null model analysis revealed the absence of regulator patterns in species associations, which could be explained to the fact that many of the species occur in most of the lakes. These results are markedly different in comparison to Patagonian lakes of Argentina and Chile that have a low crustacean species number.