Hydrodynamic conditions play a crucial role in governing microplastic (MP) transport, deposition, and resuspension in riverine habitats. However, their specific effects across distinct flow zones remain poorly understood. This study investigated how two key hydraulic indices, the Froude number (Fr) and Reynolds number (Re), influence the spatial and seasonal distribution of MPs in pools/backwaters and runs/riffles of three subtropical urban rivers in the Eastern Cape Province, South Africa. Microplastics were sampled from suspended fractions in surface water and settled fractions from the riverbed during dry/cold and wet/hot seasons. Identification was performed using chemical digestion, density separation, stereomicroscopy, and FTIR-ATR spectroscopy. Results revealed that settled MPs were strongly influenced by hydraulic conditions, with Fr being the most consistent predictor across habitats. In run/riffle zones during the wet/hot season, higher Fr values were associated with significantly lower settled MP concentrations (p < 0.001), suggesting enhanced flushing and reduced retention under more energetic flow conditions. Additionally, Fr was the only hydraulic index linked to changes in the size distribution of settled MPs (multivariate p = 0.009), primarily driven by the 1-2 mm size class (p = 0.007). In contrast, suspended MPs exhibited weaker and more variable relationships with both Fr and Re, suggesting that once MPs are entrained in the water column, turbulence and mixing processes dominate over hydraulic sorting. Elevated Re was occasionally linked to increased resuspension in deeper pool habitats, but these patterns were inconsistent across seasons. These findings demonstrate that MP-hydraulic interactions are habitat-specific and seasonally dynamic. Understanding how Fr and Re influence MP retention and mobility offers valuable insights for refining monitoring strategies and predictive models. This knowledge is crucial for enhancing our ability to forecast MP fate and inform targeted mitigation efforts in fluvial systems.