As demand for computational resources reaches unprecedented levels, research is expanding into the use of complex material substrates for computing. In this study, we interface with a model of a hydrodynamic system, under development by a startup, as a computational reservoir and optimize its properties using an evolution in materio approach. Input data are encoded as waves applied to our shallow water reservoir, and the readout wave height is obtained at a fixed detection point. We optimized the readout times and how inputs are mapped to the wave amplitude or frequency using an evolutionary search algorithm, with the objective of maximizing the system's ability to linearly separate observations in the training data by maximizing the readout matrix determinant. Applying evolutionary methods to this reservoir system substantially improved separability on an XNOR task, in comparison to implementations with hand-selected parameters. We also applied our approach to a regression task and show that our approach improves out-of-sample accuracy. Results from this study will inform how we interface with the physical reservoir in future work, and we will use these methods to continue to optimize other aspects of the physical implementation of this system as a computational reservoir.