River-health assessments in tropical headwater systems often rely on physicochemical parameters, which may not fully capture cumulative ecological degradation under strong seasonal hydrological variability. This study evaluated river condition in the upstream segment of the Upper Konto Sub-watershed, Indonesia, using an integrated ecohydraulic framework combining physicochemical indicators, biological responses, sediment nutrient dynamics, and riparian vegetation characteristics. Water quality was assessed using the Pollution Index (PI), while ecological condition was evaluated through the Family Biotic Index (FBI) based on macroinvertebrate assemblages. Sediment nutrient concentrations, hydrological variability, substrate characteristics, and riparian vegetation conditions were analyzed during both dry and rainy seasons across nine sampling stations. The results demonstrated clear seasonal ecohydraulic effects. River discharge increased from 0.038–5.688 m³/s during the dry season to 0.23–13.404 m³/s in the rainy season, while flow velocity increased from 0.12–0.82 m/s to 0.46–1.02 m/s. Although PI classified most sites as lightly to moderately polluted, FBI values indicated fair to very poor ecological conditions, particularly during the rainy season, revealing a marked divergence between physicochemical and biological assessments. Macroinvertebrate communities were dominated by pollution-tolerant taxa, with sensitive taxa absent, indicating persistent ecological stress associated with organic pollution, sediment disturbance, and habitat degradation. Sandy sediments enriched with nitrogen, phosphorus, and potassium acted as nutrient sinks contributing to long-term ecological pressure. The study demonstrates that river condition in tropical agricultural headwaters is more accurately explained by integrating physicochemical, biological, sedimentary, and riparian indicators than by conventional water-quality assessment alone. The main limitation of the study is the spatially restricted sampling design within a single tropical watershed. The findings support broader application of ecohydraulic bioassessment in watershed monitoring and river management. The originality of this work lies in linking seasonal hydrological variability, sediment nutrient enrichment, riparian buffering, and biological degradation within a unified assessment framework for tropical headwater rivers.