Climate change is predicted to significantly alter hydrological cycles across the world, affecting runoff, streamflow, and pollutant loads from diffuse sources. The objectives of this study were to examine the impacts of climate change on streamflow, total nitrogen (TN), total phosphorus (TP), and total suspended sediment (TSS) loads in the subtropical Logan-Albert catchment, Queensland, Australia. We calibrated the Soil Water Assessment Tool (SWAT) against event monitoring data in the Logan and Albert rivers, respectively. Hydrological and water quality effects of an ensemble of 11 dynamically downscaled high-resolution climate models were assessed with SWAT under high (Representative Concentration Pathway 8.5 – RCP8.5) and intermediate (RCP4.5) emission scenarios. Streamflow decreased most in winter and spring and decreased least in summer. This followed the predicted seasonal changes for precipitation, although decreases tended to be amplified due to increasing evaporative loss. TSS, TN, and TP loads showed a similar pattern to streamflow, with the largest decreases predicted for the dry season under RCP8.5 by the 2080s. Annual TSS load decreased by 34.3 and 54.2%, TN load decreased by 29.8 and 30.5%, and TP load by 24.9 and 4.4% for the Logan and Albert sites, respectively. The results of this study indicate that for subtropical river-estuary systems, climate warming may lead to lower streamflow and contaminant loads, reduced flushing, and greater relative importance of point source loads in urbanising catchments.