This work was focused on evaluating the occurrence of endocrine-disrupting compounds (EDCs) in fish muscles, such as bisphenol analogues, personal care products, including some UV-filters and musk fragrances, and selected pesticides. A total of 238 muscle samples of three fish species (Platichthys flesus, Mugil cephalus, and Dicentrarchus labrax) of an important estuary ending in the North East Atlantic Ocean (Douro River estuary, Portugal), in different seasons of the year, was analysed. M. cephalus was the species with a greater occurrence of contaminants, mainly in fishes collected during the spring. Bisphenol A was the main bisphenol analogue detected with an average content of 23.1 μg/kg wet weight (w.w.). Among chemicals used in personal care products, galaxolide, tonalide, and 2-ethylhexyl salicylate, were the most often found, being present in 15.9% (2.2–538.4 μg/kg w. w.), 4.6% (1.1–57.8 μg/kg w. w.) and 3.4% (3.9–56.1 μg/kg w. w.) of the samples, respectively. About 14% of the samples contained residues of at least one pesticide, being alachlor, aldrin, p,p’-DDT, permethrin, and prochloraz the main chemicals observed, varying from 0.1 μg/kg w. w. (p,p’-DDT) to 37.8 μg/kg w. w. (prochloraz). The daily intake estimates of the most frequent EDCs found in the fish muscles suggested that there are no health concerns, based on the recommended weekly consumption of fish for adults.