Microplastic pollution is a widely discussed research topic. However, there remains a notable gap in studies examining its geomorphological context, particularly the occurrence of microplastics in various morphological and hydraulic units within river systems. We investigated the occurrence and distribution of microplastics in hydraulic units of two urban river systems in the Eastern Cape Province of South Africa. Selected hydraulic units largely based on morphological classification were categorized into two functional groups. These functional groups represent distinct hydrodynamic conditions that modulate instream microplastic distribution. Riffles and runs were categorized as the flush functional group hypothesized to stimulate microplastic remobilization while pools and backwaters were classified as the sink functional group hypothesized to promote microplastic sedimentation. Functional groups were described by flow hydraulics and substrate properties to test the hypothesized functions. Water and sediment samples were collected from each functional group during the wet/hot and dry/cold seasons. We found that microplastic distribution was statistically significantly different between the functional groups (p<0.05). The sink functional group had the highest microplastic occurrence on the riverbed while the flush had a relatively higher occurrence of suspended microplastics. The polymer diversity was also higher in the sink functional group. High-density polymers such as polyamide, polycarbonate, and polyvinyl chloride had low distribution and were found only in the sink functional group. Hydraulic units downstream of point emission sources had the highest occurrences of microplastics. Microplastic occurrence across the functional groups was higher during the wet/hot season. In all functional groups, fragments and fibers were dominant. Particle sizes played a vital role in shaping microplastic configuration between the functional groups. Particle sizes (<0.5) were more domiciled in the flush functional group while the larger size class (> 0.5 mm) were more domiciled in the sink functional group. Our findings suggest that the sink functional group sediments are potential hotspots for microplastic accumulation, particularly during the wet/hot season.