Background: The inadequacy of drinking water supply to households in Enugu Urban, Nigeria, has forced many to depend on unimproved water sources, thus, exposing them to infection by waterborne pathogens (WBP). Methods & Materials: A cross-sectional multi-stage sampling was adopted. Standard methods of stool samples examination was used to determine the prevalence of waterborne diseases. Well-structured close-ended questionnaire aided assessment of households’ drinking water choices, knowledge and practices. Retrospective records of waterborne diseases (WBD) from January, 2013 to December, 2016 were also reviewed. Results: A total of 403 samples were examined, 344 (85.4%) were infected with at least one WBP. Ordered by prevalence, nine genera of WBP were isolated: Escherichia (38.0%), Giardia (35.2%), Entamoeba (33.0%), Salmonella (19.9%), Proteus (13.2%), Shigella (9.4%), Klebsiella (7.4%), Enterobacter (5.5%) and Cryptosporidium (5.2%). Prevalence of WBP was highest in children within 0 - 5yrs (90.6%). Out of six communities, Ogui in Enugu North Local Government Area had the highest prevalence (91.5%) of WBP. Respondents who source their drinking water from “public wells” (OR = 2.487, CI95 1.296 -4.774), “borehole/vendors” (OR = 2.175, CI95 1.231–3.843), and those that have poor sanitation level (OR = 4.495, CI95 2.358–0.371) were significantly associated with increased odds of WBD (p < 0.05). Furthermore, having very good sanitation level (OR = 0.179, CI95 0.094–0.343), not storing drinking water (OR = 0.166, CI95 0.064–0.429), boiling drinking water (OR = 0.546, CI95 0.307–0.907), and always filtering drinking water (OR = 0.398, CI95 0.174–0.909) reduced the risk of WBD (p < 0.05). Analysis of retrospective records shows an increase in temporal trend from 2013-2015, with slight decrease in 2016. Conclusion: Against the background of this study, most households in Enugu Urban are vulnerable to consuming water contaminated at many points in their journey from source to mouth. This portrays the importance of adequate provision of safe drinking water, and need for appropriate “point of use” household water treatment and storage methods that will effectively curb the prevalence of WBD.