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The management of protected areas in karstic regions is a challenge because flooded cave systems form there and provide underground hydrological conducts that may link different zones. As a consequence, affectations to the protected areas can possibly occur as a consequence of human activities in remote areas and may therefore pass undetected. Thus, the monitoring of possible contaminants in these regions is becoming imperative. In this work, we analyze the concentration of essential (iron) and non-essential metals (cadmium and chromium) in the seagrass Thalassia testudinum that grows in Yalahau Lagoon, located in a near-to-pristine protected area of the Yucatan Peninsula, close to the rapidly developing touristic belt of the Mexican Caribbean. Salinity and silicate patterns show that Yalahau is an evaporation lagoon, where groundwater discharge is important. High iron (>400 μg/g), cadmium (>4 μg/g), and chromium (≈1 μg/g) concentrations were found in the area of highest groundwater input of the lagoon. High levels (5.1 μg/g) were also found near the town dump. In the rest of the sampling sites, metal concentrations remained near to background levels as estimated from other works. Temporal changes of concentrations in the seagrass tissues show also a local input and an input from the groundwater that could provoke an environmental problem in the Yalahau Lagoon in the near future.