Benthic macroinvertebrates are widely used as reliable indicators in river biomonitoring programs. In this study, water quality in the downstream section of the Jajrud River was assessed using benthic macroinvertebrate communities at five stations—upstream of Latyan Dam Lake, Najarkola, Afjeh, Barg-Jahan, and Saeidabad—during 2013. Seasonal sampling was conducted at each station using a Surber sampler (900 cm² area, 250 µm mesh size). Water quality was evaluated using a suite of single-metric biological indices, including EPT, EPT/C, Shannon–Wiener diversity, taxonomic richness, percentage of dominant family, Hilsenhoff Biotic Index, BMWP/ASPT, BBI, TBI, SIGNAL, and MBI, as well as multimetric indices such as MMIF, IBI, and NJIS. A total of five orders and 11 families were identified, with aquatic insects accounting for 96.87% of total abundance. The most dominant families were Baetidae (41.58%) and Chironomidae (30%). The majority of both single-metric and multimetric indices consistently indicated poor to severely degraded water quality. Low values of Shannon–Wiener diversity, taxonomic richness, and EPT, together with high Hilsenhoff and MBI scores, reflected high levels of organic pollution. Similarly, multimetric indices (MMIF, IBI, and NJIS) classified the river condition as bad, very poor, or severely disturbed. Overall, the results demonstrate substantial ecological degradation in the downstream section of the Jajrud River, highlighting the urgent need for effective management and pollution mitigation strategies to improve water quality and ecological integrity.