The effects of urbanization and watershed land-use patterns on the abundance and composition of microplastics, and their relationship with key drivers of organic matter decomposition is not well documented in tropical African river systems. We assessed microplastic contamination and quantified organic matter decomposition rates in the Nairobi River and two major tributaries draining a highly urbanized watershed. To provide a contrasting land-use context, we also examined the Ragati River within the Karatina town watershed, which is less urbanized but predominantly agricultural. Microplastic concentrations in the Nairobi River increased along an urbanization gradient, with significantly higher concentrations at downstream sites (135.2 items L⁻¹) compared to upstream locations and the Ragati River (p < 0.05). Within the Nairobi watershed, the Mathare River, whose drainage is predominantly residential, contributed disproportionately high microplastic loads (77.3 items L⁻¹) relative to other tributaries and upstream cumulative concentrations in the Nairobi River mainstem (31.2 items L⁻¹), which drains a mix of commercial, industrial, institutional and residential land uses. Microplastic composition differed between watersheds: fibers dominated in the Nairobi system, indicating strong inputs from domestic wastewater and textile-related sources, followed by foams associated with packaging and construction materials. In contrast, fibers and fragments were most prevalent in the Ragati River, likely reflecting the degradation of plastic consumer products such as bottles and containers. Organic matter decomposition rates did not follow a clear urbanization gradient but instead showed strong site-specific variability. Tensile loss rates were highest in the Mathare River (4.955 Kd d⁻¹) and at the nearest downstream site on the Nairobi River mainstem, exceeding upstream rates (0.127 ± 0.01 Kd d⁻¹) and higher than the previously predicted regional rate (0.015 Kd d⁻¹). Decomposition rates in the Ragati River were comparatively similar between sites (0.188 ± 0.03 Kd d⁻¹ upstream; 0.143 ± 0.182 Kd d⁻¹ downstream). These findings highlight the influence of urbanization and associated anthropogenic pressures on microplastic pollution, while emphasizing the role of local physico-chemical conditions in regulating organic matter processing. Multi-season monitoring across broader spatial scales is needed to better capture variability and inform targeted mitigation strategies of pollution in rapidly urbanizing tropical river systems.