This study accessed the efficiency and health risks of drinking water from different sources treated by filtration, boiling, chlorination, flocculation, and solar disinfection. The microbial quality of 45 treated water samples from boreholes, wells, and pipe-borne water was analyzed to determine treatment effectiveness and to quantify risk using quantitative microbial risk assessment. The effectiveness of each treatment method was a function of sampling sources (p < 0.05) and location (p < 0.10), chlorination and boiling being the most efficient methods (100%). Shiegella in well water samples treated by filtration and flocculation had the highest daily infection risk of 69.5 × 10−1 and 67.5 × 10−1 pppd. The annual risk of infection from Salmonella, Shigella, and Staphylococcus ranged from 7.8 × 10−1 to 1.00 pppy, exceeding the U.S. EPA annual infection benchmark (≤10−4 pppy). Salmonella, Shigella, and Staphylococcus had the highest risk of illness of 4.50 × 10−1, 3.30 × 10−1, and 9.80 × 10−1, respectively. All disease burden values exceeded the WHO disease burden benchmark (≤10−6 DALYs/pppy), with Staphylococcus and Salmonella contributing the highest disease burden of 4.71 × 10−2 and 2.13 × 10−2, DALYs/pppy. Therefore, boiling and chlorination are the best disinfection methods for the pathogens tested.