Water-level fluctuations can have significant effects on lake biological communities. Thirlmere Lakes are a group of five interconnected lakes located near Sydney. Water levels in Thirlmere Lakes have fluctuated over time, but there has been a recent decline that is of significant concern. In this study, we examined over one year the species composition and richness of zooplankton (Rotifera, Cladocera and Copepoda) and abiotic conditions in Lakes Nerrigorang and Werri Berri, two of the five Thirlmere lakes, with reference to lake water level. We recorded a total of 66 taxa of zooplankton, with the first report of the rotifer Notommata saccigera from Australia, and the first report of the rotifers Keratella javana, Lecane rhytida and Rousseletia corniculata from New South Wales. There was a marked difference in abiotic conditions between the two lakes, with more variable conditions in Lake Nerrigorang. There was a significant positive correlation between zooplankton species richness and lake water level but only for Lake Nerrigorang. Although the two lakes are closely situated and thought to be potentially connected at high water levels, they show distinct ecological characters and the effect of water-level fluctuations on zooplankton species richness seems to differ between the lakes.