The Brisbane River estuary is an anthropogenically-impacted waterway in southeast Queensland, Australia. The estuary is over 80 km long and flows through an urbanised region. It receives over 500 t per year of total nitrogen (N) from direct point-source discharges in addition to sporadic flood loads of N from an agriculturally impacted upper catchment. Comprehensive water quality monitoring data for the estuary have been collected from at least 2001. This monitoring data includes ambient nutrient concentrations in the estuary, nutrient concentration and volume of the catchment inflows, and nutrient concentration and volume of point source discharges. This long-term data from a range of sources was used to determine temporal and spatial variations in concentrations, forms, stores and loads of N along the estuary for the period 2001 to 2022. Results showed that, during low-flow periods, the store of N in the mid-upper estuary (33–81 km upstream) is significantly determined by point-source discharges to this reach, and therefore the store of N can be modelled. Model parameters are the daily point source loads, a point source load decay factor, and a background constant store. In the lower estuary (0–33 km upstream) N store can be accurately determined based on dilution with seawater, with point sources not having significant influence on total N in the reach. Total N from large flood events was found to largely pass through the estuary without detectable removal processes, delivering catchment derived N directly to coastal waters. This work informs potential application of nutrient offsets in the estuary, guiding where and when offset options will be effective to mitigate the water quality impacts of point-source nutrients. Display omitted •Managing water quality impacts of point source nitrogen in estuaries depends on flow.•In low flow, N concentration is determined by point sources and in-channel processes.•N can be modelled by decay in the upper estuary and dilution in the lower estuary.•In flood flow, diffuse nitrogen dominates load and is delivered to coastal waters.•Offsets must target the N source or location of water quality impact to match flow.