The microanalysis of elemental composition by means of energy dispersive X-ray is a biomonitoring tool to identify inorganic pollutants, owing to this the present report studies the lorica of diatoms, dinoflagellates, rotifers, cladocerans, copepods and fish scales by means of scanning electron microscopy/energy dispersive X-ray spectrometry in view of finding out which toxic metals are bio-accumulating in the aquatic ecosystems of northeastern Quintana Roo, Mexico. The study was carried in the coastal zone, where samples were collected in 16 exposed water bodies: dolines, mangroves and lagoons from 2014 to 2016. Later on, the microanalysis was undertaken for the most abundant organisms. Our results for lorica and scales evince the presence of essential trace elements and toxic metals: Ag, Al, Br, Cd, Cu, Fe, Hg, Pb and Zn. Furthermore, interpolation maps of the northeastern zone of Quintana Roo were produced for Cd, Cu, Hg, and Pb, in which critical pollution zones with Cd, Hg and Pb are pinpointed; such elements are deemed toxic for human and aquatic ecosystems’ health. As a conclusion, X-ray microanalysis in lorica and scales of species native to the State is a good indication of the presence of metals in water.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.