Background: Urbanization is an important indicator of economic growth and social change but is associated with environmental degradation, which threatens sustainable growth of African cities. One of the most vulnerable ecosystems in urban areas are wetlands. In Uganda, wetlands cover an area of 11% of the country's land area. Half of the wetland areas in Ugandan cities have been converted to industry and residential areas, and urban agriculture. There is limited information on the extent of wetland conversion or utilization for urban agriculture. The objective of this study was to investigate the extent of wetlands lost in two Ugandan cities, Wakiso and Kampala, in the last 30 years. Secondly, we demonstrate a simple methodology to monitor agriculture on encroached wetlands.Methods: Using a field survey and free remote sensing data from Landsat TM 1986 and Landsat ETM 2016 we classified the rate of wetland loss and encroachment in the last 30 years. Using MODIS NDVI 16-day composites at 500-meter spatial resolution, we generated distinctive crops and crop mixtures in the encroached wetlands for urban agriculture using the ISODATA clustering algorithm.Results: Over a 30-year period, 72,828 ha (73%) of the Wakiso-Kampala wetlands have been lost. Agriculture area on the other hand doubled. Of the new cultivation area, 16,488 ha (23%) were reclaimed from wetlands. All cultivated agriculture in Kampala was in the wetlands while in Wakiso, 73% of crop agriculture was in the wetlands. The major crops grown in these urban wetlands were banana (20%), sugarcane (22%), maize (17%), Eucalyptus trees (12%), sweet potatoes (10%), while ornamental nurseries, pine trees, vegetables and passion fruits were each at 5%.Conclusions: Current wetland exploitation for food security for urban dwellers may be a trade-off between the provision of food in the short-term and the loss of important ecosystems services in the long-term.