The Barron River drains into the Coral Sea, near Cairns, Queensland (Australia) and in comparison to other Queensland wet tropics streams, it has a relatively large catchment area of about 219,000 ha. The catchment has high fish diversity, with at least 209 estuarine and freshwater species and the Barron River Estuary is a spawning and nursery ground for a variety of fish and prawn species and supports a wide range of commercial and recreational fish species. The variance and abundance of benthic macroinvertebrates can provide valuable information on the ecological condition of a river system. Overall, the macroinvertebrate populations indicated a relatively healthy system although nutrient enrichment may be causing degradation. Reserves such as existing Fish Habitat Areas and a proposed marine park will provide ongoing protection for coastal wetlands. A series of potential management issues for the catchment and future monitoring strategies are discussed