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The Mondego River estuary demonstrates signs of pollution, but the levels of endocrine disrupting compounds (EDCs), such as the natural (17 beta-estradiol and estrone) and pharmaceutical (17 alpha-ethynylestradiol) estrogens, xenoestrogenic industrial pollutants (4-octylphenol, 4-nonylphenol, and their mono- and diethoxylates and bisphenol A), phytoestrogens (formononetin, biochanin A, daidzein, and genistein), and sitosterol were either poorly or never measured in this area. Thus, to conclude about the influx of EDCs in this estuary, water samples were taken every 2 months, during 1 year (2010) in low tide, at eight sites distributed along the estuary. Water samples (1 L) were preconcentrated in the Oasis HLB cartridges and cleaned in silica cartridges before their analysis by GC-MS. In summer, potentially hazardous amounts of estrogens (a parts per thousand 26 ng L-1), alkylphenols (a parts per thousand 11.5 mu g L-1), alkylphenolethoxylates (a parts per thousand 13 mu g L-1), and phytoestrogens (a parts per thousand 5.6 mu g L-1) were measured. These data suggest that changes in the hydrodynamics of the estuary coupled with the increase of water temperatures interfere with the amount of EDCs in the water. Complementary physicochemical parameters also point to high levels of anthropogenic pollution in this area. Globally, the estrogenic load, expressed in ethynylestradiol equivalents, attained 71.8 ng L-1 demonstrating that, all together, the measured EDCs pose important health risks for both biota and humans.