Turbulence modelling is an important issue when dealing with hydrodynamic and transport models for better simulation of the transport of dissolved or suspended substances in a body-water. It controls processes involving physical balances (salt and water temperature) and, therefore, the ecosystem equilibrium. The study arises from the need to model the turbulence more efficiently when dealing with extreme situations on the Ria de Aveiro (Portugal), a coastal lagoon shallow water system dominated by tidal transport. Because the turbulence model is coupled to the hydrodynamic and transport models, a correct estimation of the eddy viscosity is important in simulating the salt and the heat transports. The aim is to assess the performance of four turbulence schemes/models (k, k-ε, Smagorinsky’s, and k-ε/Smagorinsky’s (k-ε/Sma), where k is turbulent kinetic energy and ε the dissipation rate of the turbulent kinetic energy) associated to a coupled hydrodynamic and transport models to simulate the eddy viscosity, the salinity, and the temperature. Overall, the results point out that among the different models/schemes used, the is the one which provides a more realistic value of the eddy viscosity within the range (1–6) m2 s−1, but most probably (1–3) m2 s−1. The application of the sensitivity analysis to some non-universal k-ε/Sma parameters evidenced significant sensitivity for the eddy viscosity and the salinity and moderate sensitivity for the water temperature. A 100% adjustment of the parameter values relative to the reference, translated into variations within the range of (1, 4) m2 s−1, (0, 13) PSU, and (1, 2.20) °C, for the eddy viscosity, salinity, and water temperature, respectively.