We inferred in-stream ecosystem processes in terms of photosynthetic productivity (P), system respiration (R), and reaeration capacity (RC) from a five parameter numerical oxygen mass balance model driven by radiation, stream and air temperature, and stream depth. This was calibrated to high-resolution (15 min), long-term (2.5 years) dissolved oxygen (DO) time series for moorland and forest reaches of a third-order montane stream in Scotland. The model was multicriteria calibrated to continuous 24 h periods within the time series to identify behavioral simulations representative of ecosystem functioning. Results were evaluated using a seasonal regional sensitivity analysis and a colinearity index for parameter sensitivity. This showed that >95 % of the behavioral models for the moorland and forest sites were identifiable and able to infer in-stream processes from the DO time series for around 40% and 32% of the time period, respectively. Monthly P/R ratios <1 indicate a heterotrophic system with both sites exhibiting similar temporal patterns; with a maximum in February and a second peak during summer months. However, the estimated net ecosystem productivity suggests that the moorland reach without riparian tree cover is likely to be a much larger source of carbon to the atmosphere (122 mmol C m−2 d−1) compared to the forested reach (64 mmol C m−2 d−1). We conclude that such process-based oxygen mass balance models may be transferable tools for investigating other systems; specifically, well-oxygenated upland channels with high hydraulic roughness and lacking reaeration measurements.