Assessing the ecological condition of estuaries is essential to evaluate future change. This study aimed to assess macrobenthic faunal biodiversity and physicochemical drivers in four Australian estuaries over the last two decades. Following the significant flood events on the mid-north coast NSW, we used benthic cores to sample macrofauna in 2023, replicating a 2007 baseline survey. Samples were taken on deposition sandbanks (n=12 cores at Brunswick, Sandon, Corindi and Bellinger Rivers). Overall, total abundance and species richness declined in 2023. Macrobenthic composition showed a significant difference over time among estuaries and between years. Mysella vitrea was the most abundant species, explaining the dissimilarity between years across all estuaries. Deposit feeders dominated the functional groups, but their percentage declined in 2023. Environmental variables showed no significant differences among estuaries but significantly differed between years. DistLM showed the amount of silt and turbidity significantly correlated with the changes in community structure. The BEST model included a mix of sediment and water physicochemical variables, explaining 96.26% of the variation. These results appear to reflect the influence of sediment inputs from terrestrial run-off after rain events in estuaries. Results from this study will help inform future ecosystem impacts related to flooding events.