Stream hydrology and water quality are highly interconnected and impacted by climate, land use and geology. We examined this connection using monitoring data from 2000 to 2019 for two streams with contrasting hydrological regimes—intermittent and regulated perennial—in subtropical Queensland, Australia. Our main objective was to evaluate relationships between groundwater levels, climate and flow regulation on the hydrology and water quality of an intermittent and a regulated subtropical stream. In intermittently flowing Lockyer Creek, flow was highly dependent on groundwater levels and occurred when the aquifer was recharged to elevations exceeding the upper 90‐percentile value. With 9.4% of the catchment area in irrigated horticulture, flow in Lockyer Creek was also likely to be reduced by drawdown of the aquifer for irrigation, with no flow for 30% to 81% of days over the observation period for stations in Lockyer Creek. In contrast, flow in the mid‐Brisbane River was continuous, regulated by discharge from a large upstream dam. Nutrient and suspended sediment concentrations in Lockyer Creek were generally higher than in the mid‐Brisbane River, likely associated with runoff from agricultural areas adjacent to the stream, while the upstream dam likely reduced the concentration and variability of nutrients and suspended sediment in the mid‐Brisbane River. During periods of low flow in the mid‐Brisbane River, longitudinal changes in nutrient and suspended sediment concentrations occurred, notably a significant decrease in total and dissolved inorganic nitrogen concentrations downstream (p < 0.05), indicating a possible effect of in‐stream algal uptake and denitrification. This study highlights the impact of human modifications on stream hydrology and water quality in the face of climate change. The findings can inform decision‐making on groundwater irrigation or dam release control for water security.