The design and performance characteristics of municipal drinking water systems can profoundly influence public health. To assess the operational attributes of an Accra, Ghana drinking water distribution system, high-throughput 454 pyrosequencing was employed to characterize its bacterial community composition. Samples from the waterworks and four household sources (one household tap and three polytank storage units) were analyzed within one of the Accra's distribution networks over a 4-month period. Samples provided between 9,059 and 20,076 reads (average = 13,056) that represented a broad range of bacterial diversity, including rare genera. Minimal Entropy Decomposition (MED) analysis showed that the sequences described four major assemblages. Assemblages 1 and 2 dominated the waterworks and household tap samples while polytank storage unit samples, with one exception, contained assemblages 3 or 4. The considerable bacterial taxonomic difference between different sources suggests that contamination and/or selective growth shapes bacterial community structures after treatment at the waterworks. Of particular interest are the major differences between the polytank samples following storage and the tap/waterworks samples, suggesting that water storage (stagnation) can select for unique microbial populations.