Coastal seas represent one of the most valuable and vulnerable habitats on Earth. Understanding biological productivity in these dynamic regions is vital to understanding how they may influence and be affected by climate change. A key metric to this end is net community production (NCP), the net effect of autotrophy and heterotrophy; however accurate estimation of NCP has proved to be a difficult task. Presented here is a thorough exploration and sensitivity analysis of an oxygen mass-balance-based NCP estimation technique applied to the Warp Anchorage monitoring station, which is a permanently well-mixed shallow area within the River Thames plume. We have developed an open-source software package for calculating NCP estimates and air–sea gas flux. Our study site is identified as a region of net heterotrophy with strong seasonal variability. The annual cumulative net community oxygen production is calculated as (−5 ± 2.5) mol m−2 a−1. Short-term daily variability in oxygen is demonstrated to make accurate individual daily estimates challenging. The effects of bubble-induced supersaturation is shown to have a large influence on cumulative annual estimates and is the source of much uncertainty.