The increasing installation of desalination plants in Chile raises questions about the impact of hypersaline discharges on local marine organisms. This study analyzes the effect of salinity variation on the movement of larvae of *Concholepas concholepas* (loco) and *Loxechinus albus* (red sea urchin), species of high ecological and economic importance. Using data obtained from video recordings of experimental bioassays, a database of two-dimensional trajectories was constructed, processed, and characterized using kinematic metrics. In the first stage, classical and functional statistical analyses were applied to identify mass movement variables sensitive to changes in saline conditions. The results showed significant differences between salinity levels, demonstrating that these variations alter locomotion patterns in a manner dependent on the species and the experimental context. Subsequently, a simple stochastic model was proposed to describe larval mobility, based on mean reversion processes (Ornstein–Uhlenbeck and Cox–Ingersoll–Ross). Parameter calibration and the resulting simulations allowed for the qualitative reproduction of trajectories with characteristics slightly similar to those observed experimentally, establishing an initial mathematical framework for quantifying the effect of salinity on larval dynamics. This work provides a foundation for future studies aimed at making the models more complex, incorporating specific tools based on the behavioral patterns revealed by the data, thus refining the understanding of the biological response to these environmental disturbances.