This study examined the spatial variation of potential gastrointestinal pathogens within drinking water sources and home storage containers in four neighborhoods in Maroua, Cameroon. Samples were collected from source (n= 28) and home containers (n= 60) in each study neighborhood. Pathogen contamination was assessed using quantitative polymerase chain reaction, targeting Campylobacter spp., Shiga toxin producing Escherichia coli (virulence genes, stx1 and stx2), and Salmonella spp. Microbial source tracking (MST) targeted three different host-specific markers: HF183 (human), Rum2Bac (ruminant) and GFD (poultry) to identify contamination sources. Staphylococcus aureus and the tetracycline-resistance gene (tetQ) were assessed to measure human hand contact and presence of antibiotic-resistant bacteria. Pathogen/MST levels were compared statistically and spatially, and neighborhood variation was compared with previously collected demographic information. All the test fecal markers and pathogens (except Arcobacter) were detected in home and source samples. Two neighborhoods tested positive for most pathogens/MST while the others only tested positive for one or two. Spatial variation of pathogens/MST existed between sources, storage containers, and neighborhoods. Differing population density and ethno-economic characteristics could potentially explain variation. Future research should explore the influence of demographic and ethno-economic factors on water quality during microbial risk assessments in urban Africa.