Aquatic communities across the Eurasian steppe face increasing anthropogenic pressures due to rapid population growth, catchment-wide land-use changes, and climate change. The particular type, intensity, overlay, and legacy of impacts along longitudinal gradients of Eurasian river networks provide a unique setting to investigate ecological responses in identifiable multiple stressor environments. We studied macroinvertebrate communities along the Kharaa River, Mongolia, which display a distinct, downstream gradient of moderate nutrient enrichment, disturbed bank morphology, reduced riparian vegetation, elevated turbidity, increased fine sediment substrate proportions, and fine sediment intrusion into the hyporheic zone. Within the encountered ranges of physical and chemical environmental factors (TP 0.02–0.09 mg/L, TN 0.33–0.96 mg/L, conductivity 167–322 µS/cm, formazin nephelometric units 0.62–5.43) and hyporheic fine sediment intrusion (0.9–1.6 g dry weight [DW]·L⁻¹·day⁻¹) the population densities and biomass of macroinvertebrates were high (5,313 ± 410 individuals/m² and 2,656 ± 152 mg DW/m²) and notably stable. In contrast, macroinvertebrate community structure showed strong and statistically significant negative linear relationships (Pearson's r) with turbidity, that is, for taxa richness (r = −.83), Shannon index of diversity (r = −.89), Evenness (r = −.86), the relative abundance of Ephemeroptera, Plecoptera, and Trichoptera (EPT) individuals (r = −.93) and relative biomass of hard substrate colonizers (r = −.86). The relative biomasses of fine substrate colonizers, as well as Chironomidae and Oligochaeta (both r =.76), were positively correlated with mean turbidity values. In addition, the Proportion of Sediment-sensitive Invertebrates (PSI) methodology was adjusted for local application and the resulting index scores followed a similar pattern, with PSI also being significantly correlated (r =.66) with the relative abundance of EPT individuals, the latter being the most sensitive macroinvertebrate community index. We conclude that fine sediment load is the key factor for shaping macroinvertebrate community structure in the multistressor setting of the Kharaa River followed by hydromorphological habitat complexity determined by shear stress, substrate, and grain size distributions. We suggest that the implementation of effective regional management strategies aiming at the reduction of fine sediment pollution should be given the highest priority.