A l-D tidally resolving hydrodynamic model of the Tweed Estuary has been encoded using the Estuarine Contaminant Simulator, ECoS. The model results of axial and time series variations in water elevation, salinity and turbidity are compared to field data recorded during the LOIS survey programme. The organic and inorganic controls on estuarine pH have also been investigated by encoding a new template to predict the effect of changing salinity and temperature on the pH of estuarine water. The template has been coupled to the hydrodynamic model to predict pH variations in the estuary. The model results have shown conservative behaviour of the inorganic carbon system through out the majority of the estuary, but also identified an area of potentially high photosynthetic activity near the limit of saline intrusion during periods of low summer flows. Low (< 2 ^g 1"') concentrations of chlorophyll a in the water column and increases in pH correlated with tidal inundation of the river estuary banks imply that benthic photosynthetic process are important water chemistry in the upper estuary. The effects of salinity, turbidity and pH on Kd(Cd) and K<i(Zn) has been investigated using radiotracer incubation experiments and analytically determined measurements. The results show a reduction in IQ with increased salinity, but that the K<iS determined analytically are an order of magnitude higher than those measured when radiotracers are used. Analytically determined K<iS are reduced with increasing SPM concentration and increased at higher pH. Although no photosynthetically mediated control of radiotracer uptake was identified partitioning was significantly reduced (> 90 %) when a metabolic inhibitor was added. The Kd has been encoded as an exchange transfer and used to predict axial distributions and the flux of these metals from the riverine catchment to the sea. Model results indicate that the partition coefficients determined fi-om the radiotracer studies can not fully account for the analytically determined distribution between phases. It is hypothesised that colloids and Fe-Mn oxides precipitates play a significant role in trace metal transpon in low turbidity, high pH conditions. The results have implications for the measurement and modelling of chemical fluxes in low turbidity systems.