An extensive study on the distribution of natural radionuclides in an estuarine ecosystem located in Southwestern Spain is presented. This environment is highly affected by the wastes released by a phosphoric acid industry which uses phosphate rocks as raw material for fertilizer production. This rock has generally high concentrations of U and its daughters. The estuary is formed by two rivers, Odiel and Tinto, which have a common mouth into the Atlanic Ocean and a salt marsh (Odiel marsh) affected by the income of Odiel riverwaters. This river receives directly the liquid and part of the solid (gypsum) wastes released from the industries. Besides that, most of the phosphogypsum wastes are stored in uncovered piles at the right margin of the Tinto river. The study has concluded that the wastes from such industries are the cause of the enhanced concentrations found at the bed of both river channels as well as the enhancement found in surface soils in certain zones of the Odiel wet marshland. Indeed, the Northern marsh and the Mojarrera channel at the Odiel marsh seem to be the main sinks of the contaminant released by the phosphoric acid industry.