This dataset contains NetCDF output from several model runs of a coupled physical biogeochemical model of the Hauraki Gulf in Aotearoa, New Zealand.  These model outputs were used in the paper: Macdonald, Helen Skye, Charine Collins, David Plew, John Zeldis, and Niall Broekhuizen. "Modelling the biogeochemical footprint of rivers in the Hauraki Gulf, New Zealand." Frontiers in Marine Science 10: 1041. The model simulations are performed using the Regional Ocean Modelling system with the Fennel model activated to include biogeochemical interactions. The horizontal grid spacing is 750 m with 30 vertical grid cells. Model runs span the time interval between January 2004 to December 2013. Outputs are 12-hourly averages that are divided up into files of approximately 6 months in length. These files are labelled sequentially from 1 to 20. Model simulations were performed which varied the riverine inputs: time-varying riverine inputs (called varying), a constant average riverine input (called fixed) and no riverine inputs (called no_river). This was done for both physics and biological parameters. Several different outputs are included in this dataset: Timeseries of temperature and salinity are included for a point source (175.29 OE, -36.77 OE) for all simulations (varying, fixed, no_river). Timeseries of all model state variables and advective fluxes for stations along 2 transects for the time-varying river. These transects are marked on the figure (red lines labelled “T1” and “T2”). Each station in the transect is labelled by the number of the grid-cell. For T1 this is 70-110 with numbers increasing west to east and for T2 this is 119 to 172 with numbers increasing north to south.  Geospatial time series of Bottom denitrification fluxes.  Timeseries of chlorophyll, NO3 and NH4 for 13 stations along a 3rd transect (marked as a black line with dots indicating individual stations in the figure) for the time-varying river.  These stations are labelled A through O for stations from south to north. Geospatial time series of surface and near bottom fields for temperature, salinity and velocities for simulations with and without riverine inputs (varying and no_river folders respectively).  Geospatial time series of surface and near bottom fields for NO3, NH4 and chlorophyll (biological variables) for simulations with and without riverine inputs (varying and no_river folders respectively).  Average surface and near bottom dye concentrations from a dye tracer continuously released in 3 main rivers (The Waihou, Piako and Kaueranga Rivers, marked as red * in the figure). These rivers are located in the southern end of the Hauraki Gulf (the Firth on Thames). The average surface and near bottom concentration of a dye released from all other rivers in this region is also included.  All files are in NetCDF format and contain information on the position, time and units of each data point.