Paraquat dichloride is a broad-spectrum herbicide used worldwide. It is very fast acting and used to kill a wide range of grasses and broad-leaved weeds. Paraquat dichloride gets run off to aquatic water bodies, and its presence has been reported by various researchers, where its effect is certain on aquatic organisms. Fish are vulnerable to aquatic pollutants as they are in direct contact with their environment. Therefore, our study was designed to evaluate the effects of herbicide paraquat dichloride on histology of vital organs (gills, liver, and kidney) of the fresh water fish Channa punctatus (Bloch). Toxicity effects are evaluated under static renewal test conditions, and histological alterations were detected microscopically. Fish were exposed to acute dose (96hLC50/2 = 32.93 mg/L) for 96 h of paraquat dichloride. Simultaneous control was also maintained. Principal histopathological alterations in gills during acute exposure showed curling of secondary lamellae, aneurysm, gill bridging, and enlargement of the cartilaginous core. The tissue damages like melanomacrophage centers, pyknotic nucleus, large sinusoidal congestion, and cell fusion are some histological alterations observed in the liver after acute exposure. The changes in histoarchitecture observed in the kidney include an increase in Bowman's space, necrosis of glomeruli, and damage to collecting duct at acute exposure. The histopathological changes were more prominent with the duration of exposure in the experimental groups. The present study demonstrated that the vital organs exhibited significant damage, among all gill histology specifically got altered being directly exposed to paraquat dichloride. Paraquat dichloride exposure affects the histology of gills, liver, and kidney, thus impairing the vital functions like respiration, excretion, and metabolic regulation which in turn will affect the fish health and is a serious threat. Histopathological alteration in gills, liver, and kidney can be regarded as sensitive biomarkers of paraquat dichloride toxicological manifestations and thus can be utilized for ecotoxicological biomonitoring of aquatic bodies. Graphical abstract.