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The quality of groundwater is threatened in karstic regions with very high population growth, such as the eastern coast of Yucatan. As polluted groundwater flows towards the ocean, coastal ecosystems and coral reefs may also be affected. Pollution and the interaction between the coastal aquifer and the reef lagoon were assessed at a developing area (Puerto Morelos, NE Yucatan Peninsula) within the Mesoamerican Coral Reef System. Coastal environments along the land–sea gradient (wells, mangroves, beaches, submarine springs, the reef lagoon, and the open sea) were sampled. Silicate and salinity were used as tracers of groundwater and seawater, respectively. Their patterns evidence water flow and mixing among these coastal environments. High nitrate concentrations (268.6 μM) and coliform bacteria densities indicate groundwater pollution in most of the wells sampled and also in mangroves, beaches, and submarine springs. Phosphorous content peaks (14.2 μM) in mangroves, where it is likely released due to reducing conditions in the sediments. Nitrogen flux toward the lagoon reef through groundwater discharge is estimated at 2.4 ton N km−1 year−1 and phosphorous at 75 to 217 kg P km−1 year−1. These results provide evidence of the need for more detailed groundwater studies and for the integrated management of aquifers and coastal ecosystems in karstic regions.