The presence of microplastics in freshwater ecosystems poses emerging ecological and public health challenges, yet integrative studies in tropical river systems remain limited. This study assessed microplastic accumulation, genotoxicity, and gill histopathological alterations in wild herbivorous fishes across three segments of the Brantas River in Malang, Indonesia, representing increasing gradients of anthropogenic pressure. A total of 54 fish from six species were analyzed using a multi-biomarker approach involving microplastic quantification from digestive tracts, micronucleus assays on peripheral erythrocytes, and histopathological scoring of gill tissues. Results revealed significantly higher microplastic loads (p < 0.001), micronucleus frequencies (p < 0.01), and gill damage scores (p < 0.001) in fish from downstream sites, indicating cumulative pollutant exposure. Fiber-type microplastics were most prevalent, with evidence of bioaccumulation in larger, benthic-feeding species. These findings suggest localized ecological risks and early biological impacts in species critical to riverine food webs. Notably, given that these fish species are consumed by local communities, the study highlights potential human health concerns related to microplastic exposure and associated toxicants. Recommendations include enhancing wastewater treatment, regulating plastic-based product discharge, and implementing biomonitoring programs that integrate genotoxic and histopathological markers. This work contributes to the growing understanding of microplastic impacts in tropical freshwater systems and informs both environmental risk assessment and public health protection efforts in densely populated river basins.