<p>Tropical riverine systems support diverse benthic macroinvertebrate communities that contribute to ecosystem functioning. However, these communities are increasingly vulnerable to anthropogenic disturbances, which can alter their taxonomic structure and functional trait composition. The Agusan River Basin (ARB) in Mindanao, Philippines—a socioeconomically important yet ecologically threatened system—has demonstrated signs of ecological degradation, primarily due to upstream deforestation, mining, and agricultural activities. This study examined the taxonomic and functional responses of benthic macroinvertebrate assemblages across seven rivers in the ARB under a gradient of agricultural land use to evaluate early signs of functional decline. Twelve environmental variables were measured, revealing significant differences in velocity, discharge, temperature, dissolved oxygen, pH, biological oxygen demand (BOD), chloride, phosphate, total suspended solids (TSS), and conductivity. Taxonomic analyses indicated a significant difference in species richness, while functional diversity analyses demonstrated considerable variation in functional richness. RLQ and fourth-corner analyses identified key trait–environment associations: large body size and cemented eggs were linked to cooler, faster-flowing sites with higher phosphate levels; flattened bodies and grazing behaviors were connected to warmer, slower waters; and streamlined bodies and small sizes were associated with high suspended solids. These findings suggest that anthropogenic pressures in the ARB are selecting for energy-conserving and stress-tolerant traits, potentially indicating early impairment of ecosystem functioning. The decline in functional richness and the dominance of conservative traits may reduce ecological resilience and alter population dynamics. Immediate conservation actions are essential to prevent further functional degradation and sustain biodiversity and ecosystem services in the ARB.</p>