Pollution of aquatic ecosystems by heavy metals is a major environmental problem solving, because their analysis and interpretation on the relevance has finally resorting to biological matrices developed in natural environments. The aim of this research was to assess the ecotoxicology by exposure to heavy metals in the ecosystem San Juan Santiago de Cuba -Cuba. To do an investigation which lasted from May to November 2015, understanding this time the rainy period was performed. Abiotic sampling water matrix and the species was Gambusia punctata random probability, while quantitative technique used corresponded to structured observation. Continuous quantitative variables corresponded to dissolved oxygen, pH, electrical conductivity total solids, total alkalinity, total hardness and who were determined in-situ. In the case of chemical and biochemical oxygen demands they were analyzed under laboratory conditions. Concentrations of Cu, Zn, Pb and Cd were determined in water and bioaccumulate in gills, liver and brain BioMonitor. Wet elements quantitated by atomic absorption spectrometry by inductively coupled plasma axial view. It was noted that in general physicochemical parameters were found outside the allowable value by the regulatory standard used and in the case of the elements showed bioavailable concentrations, then finding bioaccumulate in target organs. Among the stations no statistically significant differences ( p ≤ 0.05 ) and can be interpreted as persistence and mobility conditions were observed in similar form. It was concluded that the waters of the San Juan ecosystem showed physicochemical to the availability of metals, conditions can be corroborated by bioaccumulation in the tissues analyzed, because there was ecotoxicological risk for the species that develops in a natural environment.Keywords: biomarkers , ecotoxicology, San Juan ecosystem, Gambusia punctata; chemical speciation, heavy metals, Santiago de Cuba -Cuba resumen La contaminación de los ecosistemas acuáticos por metales pesados es uno de los principales problemas ambientales por resolver, por cuanto su análisis e interpretación es sobre la relevancia en recurrir finalmente, a las matrices biológicas desarrolladas en ambientes naturales. El objetivo