Water is a global need for the health and survival of all life forms and a habitat to some. However, approximately one billion people in developing countries do not have access to safe drinking water in which Namibia is not an exception. Rural communities of Ohangwena and Omusati regions of Namibia construct hand-dug wells as a source of water. However, these hand-dug wells are not monitored for water quality and are generally poorly constructed. In addition, these hand-dug wells are easily accessed by both humans and animals making them a potential reservoir for zoonotic bacteria partly known to aid antimicrobial resistance development, a global health concern. A metagenomics analysis targeting the 16S rRNA gene was used to detect the bacterial communities in a total of 40 hand-dug well water samples, with 20 being from the wet season and the rest from the dry season. A total of 57 bacterial pathogens were detected with a diverse of zoonotic assemblage. Analysis revealed significant differences in diversity and evenness, and no significant difference in richness of zoonotic bacterial pathogens in hand-dug wells between the wet and dry seasons (P < 0.05) with the dry season having a higher diversity and evenness compared to the wet season. The analysis showed that the hand-dug well water was not definitely safe for human and livestock consumption and their exposure to zoonotic pathogens was pronounced in the dry season.