In large areas of sub-Saharan Africa crop production must cope with low soil fertility. To increase soil fertility, the application of biochar (charred biomass) has been suggested. In urban areas, untreated waste water is widely used for irrigation because it is a nutrient-rich year-round water source. Uncertainty exists regarding the interactions between soil properties, biochar, waste water and fertilization over time. The aims of this study were to determine these interactions in two typical sandy, soil organic carbon (SOC) and nutrient depleted soils under urban vegetable production in Tamale (Ghana) and Ouagadougou (Burkina Faso) over two years. The addition of biochar at 2 kg m-2 made from rice husks and corn cobs initially doubled SOC stocks but SOC losses of 35% occurred thereafter. Both biochar types had no effect on soil pH, phosphorous availability and effective cation exchange capacity (CEC) but rice husk biochar retained nitrogen (N). Irrigation with domestic waste water increased soil pH and exchangeable sodium over time. Inorganic fertilization alone acidified soils, increased available phosphorous and decreased base saturation. Organic fertilization increased SOC, N and CEC. The results from both locations demonstrate that the effects of biochar and waste water were less pronounced than reported elsewhere.