This paper describes the development of a two-dimensional water quality model that solves hydrodynamic equations tied to transport equations with reactions mechanisms inherent in the processes. This enables us to perform an accurate assessment of the pollution in a coastal ecosystem. The model was developed with data drawn from the ecosystem found in Mexico’s southeast state of Tabasco. The coastal ecosystem consists of the interaction of El Yucateco lagoon with Chicozapote and Tonalá rivers that connect the lagoon with the Gulf of Mexico. The results of pollutants transport simulation in the coastal ecosystem are presented, focusing on toxic parameters for two hydrodynamic scenarios: wet and dry seasons. As it is of interest in the zone, the transport of four metals is studied: Cadmium, Chromium, Nickel, and Lead. In order to address these objectives, a self-posed mathematical problem is solved numerically, which is based on the measured data. The performed simulations show how to characterise metals transport with an acceptable accuracy, agreeing well with measured data in total concentrations in four control points along the water body. Although for the accurate implementation of the hydrodynamic-based water quality model herein presented boundary (geometry, tides, wind, etc.) and initial (concentrations measurements) conditions are required, it poses an excellent option when the distribution of solutes with high accuracy is required, easing environmental, economic, and social management of coastal ecosystems. It ought to be remarked that this constitutes a robust differential equation-based water quality model for the transport of heavy metals. Models with these characteristics are not common to be found elsewhere.