The current study aimed to investigate the ectoparasitic diversity and gill alterations in Hoplerythrinus unitaeniatus (Characiformes: Erythrinidae) and Cichlasoma bimaculatum (Perciformes: Cichlidae) and evaluate the microbiological and physicochemical quality of water samples deriving from a Quilombola zone in Maranhão State, Brazil. Water samples and 42 fish specimens, 21 H. unitaeniatus and 21 C. bimaculatum, were collected from a floodable environment. Water samples were subjected to physicochemical and microbiological analyses in the laboratory environment. Fish specimens were euthanized to collect and identify ectoparasites in animals' mucus, body surface, and gills, as well as to enable the histological analysis of the second right gill arch. The herein-identified ectoparasites have shown 30.95% prevalence and comprised three phyla: Platyhelminthes, Trematoda and Arthropoda. The herein-identified main histological changes comprised incomplete and complete fusion of several lamellae, lifting of respiratory epithelium, lamellar disorganization, lamellar epithelial hyperplasia, and blood sinus dilation. The herein calculated histological alteration index has shown that 23.80% of specimens presented mild-to-moderate tissue damage, 4.77% presented moderate-to-severe tissue changes, and 9.52% presented irreparable tissue damage. It was possible concluding that histological gill lesions identified in fish specimens analyzed may be adaptive responses to the affected environment and the incidence of ectoparasites.