Floodplains are highly complex ecosystems representing high biodiversity and conservation values, but they are also one of the world’s most threatened ecosystems due to extensive development and anthropogenic activities. Lake Tempe is a lowland riverine floodplain lake in Sulawesi Island, Indonesia, that is subject to multiple stressors such as flow alteration, eutrophication and invasive species. In this study, the dynamics of the zooplankton community size structure was investigated in Lake Tempe. Five size-based metrics, including zooplankton mean body size, total abundance, total, biomass, and normalised biomass size spectra (NBSS) slope and intercept were assessed from net-sampled zooplankton collected monthly from March to December 2016, and the role of environmental variables in shaping these size-based metrics were also examined. Zooplankton community size structure is a useful metric as it is less labour intensive than traditional approaches, provides more data accuracy and does not require highly specialised taxonomic expertise. The zooplankton community in Lake Tempe was characterised by high density of small-sized zooplankton with an average mean body size < 500 µm equivalent spherical diameter. While the zooplankton density was characterised by the dominance of the size class 300–700 µm, there was evidence of a significant contribution of the size > 700 µm towards total biomass. Seasonal hydrological regimes, water temperature and eutrophication parameters, as indicated by total phosphorus and chlorophyll-a concentration, had a significant role in driving the variability of zooplankton community size structure in this system. The results of this study are not only a significant step in providing critical baseline information on the zooplankton assemblage of Lake Tempe, but is also a significant contribution to the overall understanding of zooplankton community structure in tropical lakes, and will aid in improving lake management plans in these regions.