Understanding the factors influencing biodiversity of aquatic organisms and their geographical distributions is important for the conservation of wetlands and their dependent biota. We studied the species richness of aquatic microinvertebrates such as rotifers, cladocerans and copepods in 36 inland floodplain wetlands across the Lachlan catchment in the southern Murray-Darling Basin of Australia (longitudinal range: 144.1-149.9 °E, latitudinal range: 32.9-34.8 °S, elevational range: 72-1151 m). For each animal group, we used a negative-binomial, generalized linear model to examine the relationship of species richness with longitude, latitude and elevation. By fitting quadratic expressions, we found a group-specific relationship of species richness with longitude, latitude and elevation. Our results suggest that there may be trade-offs in conserving the species richness of aquatic microinvertebrates. If conservation efforts are targeted to some specific wetlands, this may positively affect some but negatively affect other groups, depending on the location of the geographical areas subject to conservation efforts.