This research study presents enhancements to the hydro-environmental model Environmental Fluid Dynamics Code (EFDC), improving the predictive capabilities of the impacts of tidal range renewable proposals and dissolved phosphate concentrations in estuaries. Refinements to the representation of turbines and sluice gates, including updates to the discharge relationships used and momentum conservation were applied to the Severn Tidal Power Group’s Cardiff-Weston Barrage, providing an accurate assessment of the barrage’s potential impacts and highlighting the importance of correct hydraulic structure representation. The Severn Barrage was found to have minor impacts on peak water levels as far-field as the west coast of Scotland. The refinements reduced predicted peak water levels by up to 1 m upstream of the barrage. The applicability of the updated model in assisting with the design and optimisation of tidal lagoons was then tested by running a suite of different configurations of the Bridgwater Bay Lagoon, varying the turbine numbers from 60 to 360. It was demonstrated that additional turbines can negatively impact energy output, by reducing average generating time and generating over a lower head difference. Previous laboratory and field studies demonstrated a link between salinity and phosphate sorption to sediments due to the competition for sorption sites between seawater anions and phosphate. Since sediment-associated nutrients are not readily available for biological uptake, the dissolved proportion of phosphate is of particular importance when trying to predict the grown of phytoplankton and the potential for eutrophication. The salinity-linked sorption relationship was incorporated into the EFDC model to improve the prediction for dissolved phosphate across the estuary by taking into account the salinity variation. The refinement to the numerical calculation for the phosphate partition coefficient in the model caused a measurable change to the predicted dissolved phosphate levels, bringing them closer to measured data from the estuary.