In low income settlements where the quality of drinking water is highly contaminated due to poor hygienic practices at community and household levels, there is need for appropriate, simple, affordable and environmentally sustainable household water treatment technology. Solar water disinfection (SODIS) that utilizes both the thermal and ultra-violet effect of solar radiation to disinfect water can be used to treat small quantities of water at household level to improve its bacteriological quality for drinking purposes. This study investigated the efficacy of the SODIS treatment method in Uganda and determined the optimal condition for effective disinfection. Results of raw water samples from the study area showed deterioration in bacteriological quality of water moved from source to the household; from 3 to 36 cfu/100 mL for tap water and 75 to 126 cfu/100 mL for spring water, using thermotolerant coliforms (TTCs) as indicator microorganisms. SODIS experiments showed over 99.9% inactivation of TTCs in 6 h of exposure, with a threshold temperature of 39.5 ± 0.7°C at about 12:00 noon, in the sun during a clear sunny day. A mathematical optimal condition model for effective disinfection has been calibrated to predict the decline of the number of viable microorganisms over time.