Many urban farmers in Accra collect irrigation water from streams and open drains, which they store in small, on-farm ponds before use. Given that this water can be highly contaminated with wastewater, another potential role of the ponds is to disinfect irrigation water prior to use. To better understand the factors influencing bacteria and virus removal in these small ponds, we investigated the removal of culturable fecal indicator bacteria (Escherichia coli and enterococci) and coliphage (F+ and somatic coliphage) in a single batch of water stored for 3 days. Sunlight exposure was found to be important for removal. Bacteria and coliphage removal rates were faster in shallow sun-exposed water than in deeper water, due to sunlight attenuation with depth. Bacteria removal rates varied depending on solar irradiation, and correlations between total daily UVB fluence and bacteria removal rates were observed. Coliphage removal was observed in sun-exposed water but not in dark controls that allowed for sedimentation, further highlighting the importance of sunlight-mediated processes. These small ponds appear to have similar disinfection processes to larger-scale waste stabilization ponds, but can have more efficient inactivation due to their shallow depth and operation as batch reactors. Design and management recommendations for on-farm ponds are discussed.