There is limited information available on the ecology of planktonic invertebrate assemblages of small tropical lowland rivers, despite zooplankton being a vital resource for larval fish. Herein we describe the spatial patterns and temporal dynamics of invertebrate zooplankton at 8 locations over a 25-month period in the lowland section of a short coastal river in the Australian Wet Tropics. Zooplankton were more abundant in slack than flowing waters and assemblages were dominated by Copepoda, but contained many less numerous taxa, including freshwater invertebrates at the more upstream sites. Taxonomic richness, total density and the densities of the most abundant taxa were greatest in the most downstream sites. Seasonal patterns in the density of zooplankton did not differ between the 2 years. Distance-based linear modelling of assemblages identified distance downstream and associated variables, such as salinity, as the most important environmental effects on zooplankton. The zooplankton assemblage in the lower Mulgrave River is strongly influenced by the incised nature of the river, perennial flows, the presence of slack waters, wet season floods and estuarine incursion. Zooplankton dynamics differ from the typical pattern of tropical floodplain systems in that their maximum proliferation occurs during the benign but productive late dry season.