We investigated the biophysical environment, invertebrate fauna and ecosystem health of lagoons on the Tully–Murray floodplain in the Queensland Wet Tropics bioregion. These wetlands are biologically rich but have declined in area and condition with agricultural development and are poorly protected, despite being located between two World Heritage areas. Lagoons varied in size, habitats and water quality, with increasing signatures of agriculture (e.g. elevated nutrient concentrations) from the upper to lower floodplain. Zooplankton were abundant, but not diverse, and correlated variously with environmental variables, so were not useful in assessing lagoon condition. Benthic macroinvertebrates were abundant and diverse and correlated strongly with riparian condition, habitats, water quality and degree of agriculture in the catchment, but gradients in assemblage structure were not strong because the flow regime, with multiple annual floods, maintains higher water quality than in some tropical systems. The absence of pristine reference lagoons and the limited availability of replicate sites hamper the development of monitoring systems. Nevertheless, we show that appropriate sampling, analysis and knowledge of comparable systems allow inferences to be drawn regarding ecological condition. This is important because environmental managers need best available and timely advice whatever the opportunities for rigorous study design.