A model of oxygen and nitrogen biogeochemical response to hydrodynamic regimes in the Yarra River estuary

Nitrogen biogeochemical response to alternative hydrodynamic regimes in estuaries that experience frequent anoxia has major implications for coastal water quality due to the significance of denitrification as a loss pathway for bioavailable nitrogen. The efficiency of nitrogen removal and storage in estuaries is dependent on a range of hydrodynamic and biogeochemical processes, in particular, the position of the salt wedge and effect of associated regions of anoxia. The purpose of this study was to demonstrate how rapidly shifting oxygen concentrations in the periodically anoxic Yarra River estuary, Australia, drive dynamic shifts in nitrogen cycles driving nitrogen assimilation efficiency of the estuary. Unravelling the complexity of the process response of nitrogen cycles in estuaries has been difficult to undertake empirically, so a numerical modelling approach is presented here to quantitatively predict variability in nitrogen assimilation, and demonstrate use as a tool to support optimal estuarine management. A coupled 3D finite volume hydrodynamic-biogeochemical model of the estuary was developed to simulate flow, transport, mixing and biogeochemical reactions of oxygen and nitrogen, and used to quantify nitrogen cycling processes under alternative hydrodynamic regimes that occurred over a period of 12 months. The model was forced by boundary conditions that included meteorological data, inflow from two river sources and a tidally driven water level at the downstream boundary. Simulated concentrations of organic nitrogen, ammonium and nitrate were compared to measured data from field observations to evaluate model fit. Model output of both concentrations and process rates of mineralisation, nitrification, denitrification and sediment fluxes were analysed in relation to upstream nutrient loads under changing hydrodynamic regimes. The model simulated observed patterns of both seasonal and spatial variation of inorganic and organic nitrogen in the estuary. A system-level validation comparing the deviation from mixing line for both ammonia and nitrate against oxygen concentrations also paralleled patterns in observed data. Simulated patterns of oxygen and nitrogen varied significantly over the simulated period both temporally and spatially. Tidal forcing balanced by changes in upstream flow volumes drove patterns of response in oxygen and nitrogen concentrations that varied across the model domain on both episodic and seasonal time-scales. Patterns of net nitrogen flux closely matched patterns of oxygen concentration. On a temporal scale, periods of low flow led to depleted oxygen concentrations, increase in sediment ammonium flux and reduction in rates of denitrification. During the dry summer season, episodic high flow events reversed this pattern over periods of 2-7 days. It was identified that low flows generally lead to an average positive net nitrogen flux across the estuary, whereas increased flows tend to switch the system towards a net negative nitrogen flux. This application has demonstrated that utility of the model to unravelling the complex biogeochemical pathways that determine oxygen and nitrogen response to hydrodynamic regimes in a highly dynamic salt wedge estuary. Of particular interest to estuarine management is the pattern that emerged at the system-scale, whereby the volume of flow required to switch the net nitrogen budget of the estuary from positive (nitrogen source) to negative (nitrogen sink) was linked to the antecedent conditions that vary seasonally.