A continuous solar water disinfection system was designed, installed and tested in Isiolo town, Kenya. The system consisted of two flat plate solar collectors each having 2.34 m2 gross area and photovoltaic pumping system. International Organization for Standardization (ISO) analytical procedures; ISO16649-3, ISO 6888-2, ISO 4833-1, ISO 9308-, ISO 10523:2017 ISO 7027: 2016, and ISO 7887: 2011 were used to determine the quality of disinfected and untreated water. The experimental design consisted of series collectors without heat exchanger, parallel collectors without heat exchanger and series arrangement of solar collectors with heat exchanger for preheating the cold incoming water using the exiting hot water. Total coliforms, total plate count, Staphylococcus aureus and Escherichia coli log10 counts in raw water were: 3.4, 3.8, 2.3 and 2.1 respectively. The mean Log10 reductions in total coliforms, Escherichia coli, Staphylococcus aureus and total plate counts were; 3.3, 1.9, 1.9 and 3.7 respectively in series arrangement with heat exchanger. Inactivation to < 1 CFU/ml was attained using series collector’s arrangement with heat exchanger between 12:00 and 14:00. Parallel collector arrangement induced water pasteurization that required recirculation and low flow rates to effectively initiate microbiological inactivation. Staphylococcus aureus requires temperature greater than 48 °C to initiate inactivation. Series collector arrangement with heat exchanger produced 200 l of disinfected water per day. However, additional collectors and water recirculation are required to increase the volume of disinfected water.