We investigated disease trends of concern for fish or public health in a 5-y (2017-2021) prospective survey of fish in Cook County, IL, inland lakes. Lesions were assessed in relation to fish species, lake type and location, season and collection year, and lake water chemistry parameters. Fish included bullheads (n = 98), common carp (n = 99), bluegill (n = 114), and largemouth bass (n = 118). Annually, fish collection and point-source water sampling were conducted in spring, summer, and fall from both seepage and impoundment lakes. Examinations included autopsy, wet-mount cytologic assessment for ectoparasites, and histopathology. No lesions of public health concern were detected. The most common abnormalities were branchitis (261 of 429; 60.8%) and endoparasitism (312 of 429; 72.7%). Branchitis was mild in most cases (189 of 261; 72.4%) and concurrent with branchial parasitism in 175 of 261 (67%) cases. Monogeneans were the most common gill parasites but did not influence branchitis severity (Kruskal-Wallis, p = 0.484). Using generalized ordered logistic regression, predictors of branchitis severity included fish species (p < 0.001), the interaction of lake or location and alkalinity (p < 0.001), and water temperature or season (p < 0.001). Endoparasites included tissue larval trematodes (metacercaria), nematodes, and cestodes (plerocercoids), enteric acanthocephalans, gastric trematodes, renal myxosporidia, biliary and gall bladder myxosporidia, enteric cestodes, and tissue microsporidia. Using generalized ordered logistic regression, variables influencing endoparasitism severity included species (p < 0.001), year (p < 0.001), chloride level (p = 0.009), and the interaction of year and chloride level (p < 0.001). Our results suggested overall good health of fish in sampled Cook County inland lakes and provide a foundation for continued monitoring of ecosystem and public health in the urban environment.