Water-quality observations in estuaries can be highly variable in time and space, making it difficult to quantify nutrient fluxes and to discriminate patterns. We measured nitrate, phosphate and ammonium concentrations in two shallow tidally dominated estuaries in Tauranga Harbour, New Zealand, during four periods (winter, start of spring, end of spring and summer) within 1 year, to determine the source of variability observed in a 19-year monitoring program. These measurements consisted of high-frequency monitoring during one 24-h period (covering a daytime flood-ebb tide and a night-time flood-ebb tide) at each estuary. Concentrations of nitrate and ammonium had distinctive tidal patterns, with rising values during ebb flows. This tidal asymmetry caused a net seaward flux of dissolved inorganic nitrogen (nitrate and ammonium), with higher exports at night. Net fluxes were 34358kgN per tidal cycle for nitrate and 2293kgN per tidal cycle for ammonium. Fluxes were large relative to previously published model-based predictions for the region, particularly during winter. Our results showed that estuarine sampling strategies need to account for tidal variability and the role of episodic runoff events, and highlighted the importance of correctly validated mass fluxes from field measurements for comparisons with nutrient-loading models.