The description, calibration and application of a reaction-diffusion model of early diagenesis is presented. Unlike previous models it has been developed for a temperate latitude estuary (upper and lower Gt. Ouse, UK) impacted by high nitrate concentrations (annual mean 700μM). Five variables, O₂, NO₃⁻, NH₄⁺, SO₄⁻ and S⁻ are modelled from the steady state distributions of bulk total organic carbon (TOC). Different representations of the first order rate constant, k, for TOC mineralisation are tested. Use of separate k values for individual mineralisation pathways is the only way to reproduce the data but at the cost of 1) increasing the degrees of freedom in the model and 2) conceptual simplicity. This casts doubt over the universal applicability of diagenetic models in high NO3' environments. Underestimation of the observed ammonium fluxes leads to the inclusion of dissimilatory nitrate reduction to ammonium (DNRA) into a diagenetic model for the first time. Use of an empirical temperature function successfully simulates rates of denitrification and DNRA. It is concluded that temperature is an important control in partitioning nitrate reduction into DNRA and denitrification in the Gt. Ouse sediments. This temperature effect implies that during an extended warm summer in temperate estuaries receiving high nitrate inputs, nitrate reduction may contribute to, rather than counteract a eutrophication event. A literature review showing that DNRA can account for up to 100% of the nitrate reduction in different locations around the world, means that diagenetic models of the nitrogen cycle in coastal areas should include DNRA. A parameter sensitivity analysis (PSA) reveals a highly non linear model response to parameter changes of ± 50%. The variability in model response among the sites in the Gt. Ouse highlights the importance of accounting for differences in 1) the relative contributions of oxic, suboxic and anoxic mineralization to total organic carbon mineralization; 2) rates of oxygen consumption and 3) oxygen penetration depths. Organic carbon mineralization rates are most sensitive to porosity and diffusion related parameters and to literature ranges of half saturation constants which influence the rate of sulphate reduction. Variations in these parameters suggest that it is unwise to consider parameters as constant in space highlighting a possible barrier to the development of a universally robust model. The response of the model to changes in the thickness of the diffusive boundary layer (DBL, 0.0001-0.1 cm) is examined. Neglecting the presence of the DBL in core incubations may result in erroneous measurements of solute fluxes: higher oxygen (13-63%) and ammonium (13-40%) fluxes and lower nitrate (5-20%) and sulphate (20-980%) fluxes than might be occurring in situ. Thicker DDLs decrease organic carbon degradation rates (8-42%) implicating the DBL as a factor in organic carbon preservation. This contrasts with previous findings based on assumptions about oxygen consumption which do not apply in the Gt. Ouse sediments. The model is used to investigate the variability in the observed intra-annual changes in solute fluxes across the sediment-water interface (SWI). Variations in temperature and overlying concentrations of nitrate, ammonium and sulphate are insufficient to explain the measured variability. This casts doubt on a data-based assumption that concentrations of organic carbon were in steady state at all sites. It is concluded that organic carbon should be dynamically modeled in these sediments. Higher measured than predicted fluxes of oxygen and nitrate across the SWI, indicate the presence of porewater advection or enhanced transport by turbulent diffusion induced by the stirring rates in the core incubations. Inclusion of such transport processes is a recommended area for future work.