To explore the differences in the nutritional quality of the muscles of bighead carp from different environments and aquaculture systems, we investigated three types of water bodies typically used for aquaculture: A common culture pond (NC), a natural lake (PY), and a cold water reservoir (XHK). Parameters affecting quality were evaluated, including muscle microstructure, fatty acid profiles, amino acid profiles, and volatile compounds. Fish from the XHK reservoir had the smallest muscle fiber diameter and the highest muscle fiber density (25.3 fibers/0.01 mm2), while muscle fiber density was lowest in fish from the NC pond (9.7 fibers/0.01 mm2). The bighead carp from the XHK reservoir had a much wider variety of unsaturated fatty acids, as well as higher levels of total polyunsaturated fatty acids. Eicosapentaenoic acid (EPA), docosahexenoic acid (DHA), and arachidonic acid (AA) were all significantly more abundant in the XHK group, increases of 7.48%, 12.12%, and 17.49%, respectively (P < 0.05). The bighead carp from NC contained more “fishy” volatile flavor substances, as well as hydrocarbons with higher threshold values. Fish from XHK and NC had a greater umami intensity due to the presence of abundant volatiles with special aromas, including 1-Octene-3ol, DL-Menthol, and 2-ethyl-.