Microplastics are important novel pollutants in freshwaters but their behaviour in river sediments is poorly understood due to the large amounts of coloured dissolved organic matter that impede sample processing. The present study aimed to 1.) estimate the microplastic pollution dynamics in an urban river system experiencing temporal differences in river flow, and 2.) investigate the potential use of chironomids as indicators of microplastic pollution levels in degraded freshwater environments. Microplastic levels were estimated from sediment and Chironomus spp. larvae collected from various sites along the Bloukrans River system, in the Eastern Cape South Africa during the summer and winter season. River flow, water depth, channel width, substrate embeddedness and sediment organic matter were simultaneously collected from each site. The winter season was characterised by elevated microplastic abundances, likely as a result of lower energy and increased sediment deposition associated with reduced river flow. In addition, results showed that particle distribution may be governed by various other external factors, such as substrate type and sediment organic matter. The study further highlighted that deposit feeders associated with the benthic river habitats, namely Chironomus spp. ingest microplastics and that the seasonal differences in sediment microplastic dynamics were reflected in chironomid microplastic abundance. There was a positive, though weakly significant relationship between deposit feeders and sediment suggesting that deposit feeders such as Chironomus spp. larvae could serve as an important indicator of microplastic loads within freshwater ecosystems.