Plastic and, particularly, microplastic (MP) pollution is a growing research theme, dedicated largely to marine systems. Occurring at the land–sea interface, estuarine habitats such as mangroves are at risk of plastic pollution. This study compared MP pollution (level, morphotype, polymer composition, size and colour) across four South African estuaries, in relation to the built and natural environment. Mouth status, surrounding human population densities and land-use practices influenced the level and type of MP pollution. Systems that were most at risk were predominantly open estuaries surrounded by high population densities and diverse land use types. Microplastic levels and the diversity of types detected increased with increasing levels of anthropogenic disturbance. Overall, microfibres dominated in estuarine water (69%) and mangrove sediment (51%). Polyethylene (43%) and polypropylene (23%) were the dominant polymers overall. Weathered fishing gear, weathered packaging items and run-off from urban/industrial centres are probable sources of MP pollution . Increased run-off and river input during the wet/rainy season may explain the markedly higher MP loads in estuarine waters relative to the dry season. By contrast, MP deposition in mangrove sediment was higher during the dry season. Sediment MP abundance was significantly positively correlated with both pneumatophore density and sediment size (500–2000 µm). This study highlights the role of mangroves as MP sinks, which may limit movement of MPs into adjacent environments. However, under conditions such as flooding and extreme wave action, mangroves may shift from sinks to sources of plastic pollution.