Kuala Tambangan, being an estuary area with high anthropogenic activities, is prone to water quality issues. To assess its health, bioindicator species play a crucial role. Histological alterations in fish organs can indicate environmental pollutants. Boleophthalmus pectinirostris, commonly found in Kuala Tambangan estuary, is a potential bioindicator species. The study aimed to evaluate Kuala Tambangan estuary waters' quality using physical and chemical parameters through the pollution index (PI) method. Additionally, histopathological assessments of B. pectinirostris' liver and kidney were conducted. The PI method followed the Government Regulation of the Republic of Indonesia No. 22 of 2021 Annex VIII concerning seawater quality standards. Histopathological lesions were identified using the paraffin method microtechnique, which is considered the gold standard of toxicity testing. Lesions were scored and compared descriptively. Results determined PI values of 2.20 and 2.24 for water quality in two observations during July 2022 and February 2023, respectively. Mild liver and kidney alterations were characterized by necrosis, fatty degeneration, inflammation, and congestion. Based on physical and chemical data, the Kuala Tambangan estuary was classified as slightly polluted, affirming the potential of B. pectinirostris as a bioindicator species.