Background: Provision of good quality household drinking water is an important means of improving public health in rural communities especially in Africa; and is the rationale behind protecting drinking water sources and promoting healthy practices at and around such sources. Objectives: To examine the microbial content of drinking water from different types of drinking water sources in Manonyane community of Lesotho. The community’s hygienic practices around the water sources are also assessed to establish their contribution to water quality. Methods: Water samples from thirty five water sources comprising 22 springs, 6 open wells, 6 boreholes and 1 open reservoir were assessed. Total coliform and Escherichia coli bacteria were analyzed in water sampled. Results of the tests were compared with the prescribed World Health Organization desirable limits. A household survey and field observations were conducted to assess the hygienic conditions and practices at and around the water sources. Results: Total coliform were detected in 97% and Escherichia coli in 71% of the water samples. The concentration levels of Total coliform and Escherichia coli were above the permissible limits of the World Health Organization drinking water quality guidelines in each case. Protected sources had significantly less number of colony forming units (cfu) per 100 ml of water sample compared to unprotected sources (56% versus 95%, p < 0.05). Similarly in terms of Escherichia coli, protected sources had less counts (7% versus 40%, p < 0.05) compared with those from unprotected sources. Hygiene conditions and practices that seemed to potentially contribute increased total coliform and Escherichia coli counts included non protection of water sources from livestock faeces, laundry practices, and water sources being down slope of pit latrines in some cases. Conclusions: These findings suggest source water protection and good hygiene practices can improve the quality of household drinking water where disinfection is not available. The results also suggest important lines of inquiry and provide support and input for environmental and public health programmes, particularly those related to water and sanitation.