Urbanization has significantly increased globally during the last century and has far-reaching consequences for biodiversity and their associated habitats, particularly wetland ecosystems. Previous studies have focused primarily on wetlands in non-urban areas, and urban wetland biodiversity patterns are currently not well understood, particularly across Africa. Here, we investigate two highly transformed urban wetlands in Cape Town, South Africa, and determine the relative importance and influence of local environmental variables as drivers of macroinvertebrate richness and community structuring. We also determine the influence of local environmental variables for patterns of species turnover and nestedness within and among these wetlands, and provide management recommendations based on our findings. We found that few macroinvertebrate species were associated with these wetlands, yet community variation was driven by a combination of local environmental variables. Our results also indicate that the turnover component of beta diversity, rather than nestedness, was responsible for most of the variation in the overall macroinvertebrate community. We identified two major problems regarding the current ecological state of the investigated wetlands. Firstly, high nutrient loads originating from the surrounding land uses which reduced wetland biodiversity, and secondly, the transformation of these wetlands from seasonal to perennial water bodies. We recommend local and regional scale approaches to limit urban waste from entering these systems, and management of water levels simulating natural Mediterranean-type climate dynamics more closely are required to ensure that the maximum possible diversity can be supported in these wetlands.