This dissertation focuses on understanding and quantifying how environmental conditions affect the fate of salinity and mercury in freshwater. Salinity and mercury concentrations are increasing due to anthropogenic activity and threaten ecosystem services of water bodies. Management is important to prevent further degradation. To reconcile management of multiple water quality parameters with ecosystem services, an improved basic knowledge and advanced tools are important. It is still difficult to identify main drivers for elevated salinity at a specific site and there are gaps in our basic understanding of mercury cycling. Therefore, this research focused on development and application of numerical models to improve our understanding of salinity and mercury cycling and to provide tools to plan management measures. The aim of the first chapter was to continue development of a module for seasonally managed wetlands as part of a real-time forecasting tool for salinity in the San Joaquin River watershed. Revising water sources, inflow time series, and model variables that determine the timing of outflow improved model performance by better representing the extensive reuse and recirculation within wetlands. Adequate simulation of conservative water quality parameters such as salinity is a pre-requisite to simulate non-conservative parameters such as mercury. The second chapter focused on critically reviewing published kinetic rate constants for mercury methylation and demethylation including application to a reaction-transport model. Mercury exists in multiple chemical forms and monomethylmercury (MeHg) is one of the most toxic forms. Two important variables that determine MeHg concentrations are the rate of MeHg production and degradation. The critical review informs selection of rate constants from literature and provides a tool to assess rate constants. Experimental conditions and mathematical assumptions were found to cause uncertainty and limit comparability. The aim of the third chapter was to apply a kinetic-thermodynamic model to field data to evaluate how environmental conditions affect MeHg production. The chapter shows how field data can be used to constrain model parameters. A novel rate formulation was developed to simulate precipitation of Hg minerals depending on concentrations of sulfur and organic matter. The addition of the rate improved simulated MeHg under a range of sulfide concentrations. Overall, numerical models proved suitable to identify knowledge gaps and improve basic understanding for both salinity and mercury in freshwater.