Te Puna and Waikareao estuaries are shallow tidally-dominated estuaries in Tauranga Harbour located on the Bay of Plenty Coast, New Zealand. Tauranga Harbour is the site of a large commercial port surrounded by urban development. The primary aim of this thesis was to determine the variations of dissolved inorganic nitrogen concentrations and fluxes in both Te Puna and Waikareao estuaries over short time-scales in different seasons through field experiments and a dynamically coupled three-dimensional (3D) hydrodynamic-biogeochemical model. To gain insight in the short temporal variability in nutrient concentrations, 24-hourly measurements of dissolved nutrients were conducted over four periods (winter, summer, start of spring, and end of spring) within one year in Te Puna and Waikareao estuaries. The nitrate and ammonium concentrations showed distinctive tidal patterns with rising values during ebb flow. This tidal asymmetry caused a flux of DIN seaward with net fluxes ranging from 34 to 358 kg/tidal cycle of nitrate and 22 to 93 kg/tidal cycle of ammonium. The variations in concentrations observed within tidal cycles were of a similar magnitude to the variations measured over 19-years at comparable times of the year. To further understand the sources and sinks that may control the variations measured during these short-time scale experiments, the hydrodynamic-biogeochemical model, ELCOM-CAEDYM, was set-up for both Te Puna and Waikareao estuaries. Tidal exchange of water within the harbour and its sub-estuaries was shown to have an impact on the circulation patterns in various parts of Tauranga Harbour. Hence, a hydrodynamic modelling exercise of the southern basin of Tauranga Harbour was undertaken. The model results established that the salinity profiles are tidally-driven while the temperature profiles are sensitive to wind. Residence times varied across the harbour with increasing residence times in the upper reaches of the estuary and also in sub-estuaries with constricted mouths. Model simulations of Te Puna and Waikareao estuaries also showed the sensitivity of water temperature to wind. Spatial variations in DIN, DO and residence times across both the sub-estuaries were observed from model simulations. Twenty-two scenarios were simulated in both Te Puna and Waikareao estuaries by altering the forcing conditions in the model as from analysis of field measurements from the 24-hourly sampling, showed that it was difficult to differentiate between competing sources (freshwater inflows, wind mixing and sediment fluxes) of DIN input into Te Puna and Waikareao estuaries. From the scenarios, it was found that the inter-annual variation in concentration of nitrate is primarily driven by freshwater inflows, while ammonium is primarily influenced by sediment fluxes. Ammonium is sensitive to seasonal variation in temperature with higher simulated ammonium concentrations in summer. The impacts of stream discharges on estuary DIN concentrations were mostly localised to the inflow locations with minimal impact on estuary-wide concentrations due to strong tidal flushing. The modelling scenarios also demonstrated the heterogeneities in DIN concentrations from upper to lower estuary, highlighting the difficulty of monitoring estuary health using point measurements. From the modelling scenarios, groundwater was identified as a significant contributor of DIN into the estuaries, with contribution ranging from 2% to 37%. The seasonal variation in pore-water nitrate and ammonium concentrations in a tidal flat margin at Waikareao Estuary was determined. Vertical profiles of sediment pore-water were sampled in wells that were dug into the intertidal sand flat to provide snapshots of nitrate and ammonium concentrations at different times of the year. Pore-water recycling processes were an important DIN source to the estuaries during ebb tide with greatest concentration observed in mid-winter and summer. Pore-water profiles showed ammonium as the dominant form of DIN in the wells. Nitrate concentration was higher in surface sediment and ammonium dominated the mid-depth regions (25-50 cm). Long-term monitoring of Kopurereroa Stream which discharges into Waikareao Estuary, showed higher nitrate concentration than the tidal flat wells and other monitored sites. This further highlights that the primary source of nitrate into estuaries is through freshwater discharge and ammonium is dominated by sediment recycling processes. From both field experiments and modelling scenarios, it is found that dissolved nutrient concentrations were highly variable in both estuaries with distinctive tidal patterns and also seasonal variations.