Lack of water access is an issue of global importance. The WHO and UNICEF’s Joint Monitoring Program estimated that in 2015 71% of the world’s population used a safely managed drinking water source and 89% of the world’s population used an improved water source within a 30-minute round trip of home. Madagascar’s national statistics lags far behind these global statistics with 54% of the population using improved water sources, 31% using unimproved water sources, and 16% with no service at all. This research studied water access in Madagascar with self-supply Pitcher Pumps attached on hand-driven tubewells. The term self-supply in this context refers to privately owned and constructed water sources that are not financially subsidized by governments or non-governmental organizations. Self-supply is typically seen in the form of private wells in rural areas of developed countries like the United States or in developing countries in the form of shallow wells or rain water harvesting. Self-supply Pitcher Pumps are common along the coast in Madagascar in areas where the first aquifer is shallow and in sandy soil. They are ubiquitous at the site of this study, the port city of Tamatave. People in Madagascar have benefited from increased access to affordable water because of Pitcher Pumps for decades, however, there are health risks associated with consuming the water due to lead and microbial contamination of the water. This study sought to improve microbial water quality of Malagasy Pitcher Pumps by testing two different types of well head protection: 1) a partially buried short 100-mm diameter PVC pipe collar placed around the rising main, and 2) a 50-cm diameter, circular concrete apron. The study was a mixed design experiment that allowed for between subject comparisons of wells over the same time period and for within subject comparisons of the same well sites with different types of well head protection. Wells were selected for the study that had a high risk of localized pathways of contamination and low risks of aquifer contamination relative to other wells in the area. Membrane filtration was used for microbial water quality measurements and detected a wide spectrum of bacteria grown at 37◦ C. In this study, data from 690 water samples of 44 wells (with and without well protection added) over a 9 months period was analyzed. Weak but statistically significant (p ≤ 0.05) and marginally statistically significant (0.05 < p ≤ 0.10) correlations were found between bacteria concentrations and antecedent rainfall depth for wells with aprons but not for wells with a pipe collar or no protection. No statistically significant relationship was found between bacteria concentrations in wells and type of well head protection. The lack of reduction in bacteria concentrations with well head protection is likely due to the high density of on-site sanitation near the wells and the relatively shallow water table. Generally, study results indicate that there is a wide variation of bacteria concentrations both from the same well across many months and between wells that are near each other. The second observation is consistent with other studies of wells in the area. It appears as if the best solution for improving water quality from Malagasy Pitcher Pumps to a potable level is point-of-use treatment of the water.