Long-term temporal and spatial differences in benthic community structure in Port Curtis (a semi-enclosed estuary in Queensland, Australia) were examined from quantitative grab samples. A total of 2660 grabs were collected from 30 fixed sites over the 6-year study period, and 35 421 individuals and 409 species identified. Few species were highly abundant and nearly 90% were apparently undescribed. Species abundance data revealed strong ecological gradients that were principally driven by depth and sediment grain size. Depth related differences in benthos were most pronounced between the subtidal and intertidal zones, and total abundance and richness were both significantly lower in the intertidal. Total abundance and richness were also found to be significantly lower in sediments that were either extremely coarse or extremely fine. Over the 6-year period of this study, mean species richness and abundance progressively declined 72% and subsequently recovered by 68%. Similar temporal trends were displayed by all common dietary groups (filter feeders, deposit feeders, scavengers and predators), and it appears that drivers underpinning observed changes have a consistent influence at most trophic levels. Explanations for long-term trends in abundance and richness were determined through correlation analyses with key environmental variables. Both species richness and abundance were highly correlated (positively) with turbidity measurements observed 4 months previously. This finding suggests that high levels of turbidity promote recruitment and growth of benthic organisms in Port Curtis. Strong correlations between regional rainfall, freshwater inflow, nutrient and chlorophyll a concentrations, further support the hypothesis that recent changes in benthic productivity (as defined by total infaunal abundance) within the estuary are principally the result of long-term climatic cycles including El Nino events.