<p>Degradation of streamflow magnitude and water quality is increasingly reported across many rivers in Southeast Asia, a trend likely exacerbated by climate change. Groundwater inflow into streams plays a critical role in maintaining baseflow and supporting aquatic biodiversity, yet groundwater-surface water interactions remain poorly studied in Southeast Asia. This study quantifies groundwater contribution to a pristine tropical stream in the Batu Apoi Forest Reserve, Brunei Darussalam, using ²²²Radon and stable isotope techniques. Radon-based simulations revealed groundwater inflow rates ranging between 1.0 × 10⁻⁶ to 2.0 × 10⁻⁵ m³ s⁻¹ m⁻¹, with an average of 1.9 × 10⁻⁵ m³ s⁻¹ m⁻¹ contributing to 22% of the downstream discharge for the investigated 6 km reach. Preliminary stable isotope analysis (δ18O and δ2H) suggested that groundwater may account for approximately 66% of streamflow. Despite differences in methods and absolute estimates, both approaches indicate significant groundwater-surface water interaction. Water quality parameters—low turbidity, high dissolved oxygen, and moderate conductivity—indicate a pristine stream environment. These conditions, combined with substantial groundwater input, likely support the high biodiversity observed, including the presence of sensitive aquatic species. The findings highlight the ecological value of groundwater in tropical river systems and the importance of continued monitoring to assess future changes driven by climate or land-use impacts.</p>