Anthropogenic activities from industrial, residential, and agricultural areas degrade river water quality through the release of organic pollutants and heavy metals. The Welang, Gembong, and Rejoso Rivers in Pasuruan Regency, East Java, Indonesia, are freshwater ecosystems exposed to these pollution sources. This study evaluated kidney histopathological alterations in Mystus gulio as biomarkers of aquatic pollution and compared tissue damage among the three rivers. Fish were collected from three sampling stations in each river between November 2025 and February 2026. Kidney tissues were processed using the Hematoxylin–Eosin (H&E) staining method and examined microscopically at 400× magnification. Histopathological damage was assessed using a lesion-based scoring system, while water quality parameters and lead (Pb) concentrations in kidney tissues were also measured. Three major lesions were identified: congestion, degeneration, and necrosis. The highest damage occurred at Gembong River Station 3, with a histopathological score of 77% (badly damaged), whereas the lowest was recorded at Welang River Station 1 (31%, slightly damaged). Biochemical oxygen demand (BOD) and Pb concentrations exceeded permissible limits at all sampling sites, with the highest Pb concentration (1.68 mg L⁻¹) found at Gembong River Station 3. Greater Pb accumulation was associated with more severe kidney damage. These findings demonstrate that kidney histopathology in M. gulio is an effective biomarker for assessing freshwater pollution caused by heavy metal contamination.