Microanalysis of elemental composition using dispersive energy X-ray is a biomonitoring tool to identify hazard metals. Using scanning electron microscopy/energy dispersive X-ray spectrometry, we studied the bioaccumulation of toxic metals in the lorica of diatoms, dinoflagellates, rotifers, cladocerans, copepods and fish scales in the aquatic ecosystems of northeastern Quintana Roo, Mexico. The study was carried out in the coastal zone, where samples were collected in 16 exposed bodies of water, including dolines, mangroves and lagoons. Microanalysis of the most abundant organisms revealed evidence of the presence of essential trace elements and metals (Ag, Al, Br, Cd, Cu, Fe, Hg, Pb and Zn) in the lorica and scales. Furthermore, interpolation maps of the northeastern zone of Quintana Roo were produced to pinpoint critical pollution zones of Cd, Hg and Pb, elements that are deemed toxic to the health of humans and aquatic ecosystems. In conclusion, elemental microanalysis of species native to the Mexican state of Quintana Roo using X-ray is a powerful tool for aquatic and toxicological biomonitoring of hazardous metals.