Health problems associated with the consumption of untreated drinking water is one of the greatest concerns in Kabale District in spite of government’s efforts to provide safe drinking water to the people. The objective of the study was to examine household water treatment technologies (HWTS) and evaluate their ability to improve the microbial quality of drinking water. We analyzed 20 paired samples (source and treated) of drinking water from four sources of drinking water in close proximity to homesteads. Samples were analyzed for total coliforms and Escherichia coli, the indicators of faecal contamination, to measure effectiveness of HWTS. The parameters were determined using membrane filtration method. Laboratory data was statistically analyzed using one way ANOVA from SPSS software version 17.0. All HWTS improved the microbial quality of drinking water under laboratory conditions. Mean log10 total coliforms reductions were 2 log10 (99.5%) for boiling, 0.9 log10 (84.8%) for biosand filtration, 1.9 log10 (99.5%) for application of Water Guard tablets and 2 log10 (98.1%) for application of aqua safe tablets. The mean log10 Escherichia coli reductions were 1.2 log10 (100%) for boiling, bio sand filtration, application of Water Guard tablets and application of aqua safe tablets. The microbial removal effectiveness of HWTS was significantly high and the differences in the mean total coliforms reductions by different HWTS were statistically significant (P < 0.05). Water Guard, bio sand filtration, boiling and aqua safe tablets significantly remove total coliforms and Escherichia coli and should therefore is promoted at local level.