The Lima River is a Spanish–Portuguese water body. Notwithstanding the fact that the river incorporates protected natural areas, levels of endocrine-disrupting compounds (EDCs) within its waters have never been measured; such EDCs include the following: natural and pharmaceutical oestrogens (17β-estradiol, E1, and 17α-ethynylestradiol), industrial and household pollutants (4-octylphenol, 4-nonylphenol, and their monoethoxylates and diethoxylates, and bisphenol A), phytoestrogens (formononetin, biochanin A, daidzein, genistein), and phytosterols (namely, sitosterol). To obtain an understanding of levels of EDCs, water samples were taken from eight sampling sites along the river every 2 months during a 1-year period (2011). The water samples were preconcentrated (Oasis HLB cartridges), cleaned (silica cartridges), and analysed using gas chromatography. Results showed that levels of oestrogens and industrial and household pollutants were higher in summer than in other seasons. Although oestrogens were more abundant (approximately 40 ng/L) on the southern margin of the river, levels of other pollutants were higher (approximately 124 ng/L) in the north. Phytoestrogens and sitosterol showed clear seasonal fluctuations with higher amounts of formononetin (approximately 389 ng/L), biochanin A (approximately 160 ng/L), and sitosterol (≥5 µg/L) measured in summer. The overall oestrogenic load, expressed in ethynylestradiol equivalents, was 18 ng/L for oestrogens, 0.5 ng/L for industrial and household pollutants, and 13 ng/L for phytoestrogens. Water physicochemical parameters indicate anthropogenic pollution because Σnitrites,nitrates (>1 mg/L) and phosphates (approximately 0.4 mg/L) were high. The study showed that the waters of the Lima River are subject to impacts and that levels of EDCs pose risks to the river’s biota.