Like most harbors, the Port of Ensenada, Mexico, is vulnerable to the accumulation of pollutants. A wave-driven seawater pump (Sistema de Bombeo por Energía de Oleaje [SIBEO]) is proposed to inject clean and oxygen-rich water from outside the Port to promote flushing in its more stagnant areas. Three-dimensional, numerical simulations with the Estuary and Lake Computer Model (ELCOM) were used to investigate the behavior, extent, and effect of the SIBEO inflow. Conservative tracer experiments indicate that the effect of the pump would spread through the pycnocline and become noticeable throughout the harbor within a month. The tracer method yields a bulk estimate of the flushing time for the port of approximately 4 days, although the spatial variability of the flushing is significant. The least-flushed areas of the harbor are its NE and SE corners, where greater concentrations of pollutants have been observed.