Arsenic in groundwater has been a concern in South and Southeast Asia for more than a decade. We explore here the possibility that hydrogeologic factors recently shown to influence the distribution of arsenic might also affect the level of contamination of shallow (<20 m) wells with microbial pathogens. A total of 96 shallow tube wells in two nearby villages of Bangladesh were surveyed during the wet and dry seasons, along with 55 deeper wells in neighboring villages. One of the two villages is located in a particularly sandy environment where recharge is rapid and shallow wells contain little arsenic. Shallow aquifers in the other village are capped with an impermeable clay layer, recharge is an order of magnitude slower, and arsenic levels are high. The fecal indicator E. coli was detected in 43% of shallow wells, compared with 12% of deeper wells. More shallow wells contained E. coli during the wet season (61%) than during the dry season (9%). In the wet season, a higher proportion of shallow wells in the village with low arsenic levels (72%) contained E. coli compared with the village having high arsenic levels (43%). Differences in arsenic and E. coli distributions between the two sites are likely due to the differences in permeability of near-surface sediments although differences in average well-depth between the two villages (9 ± 4 vs. 15 ± 3 m) may play a role as well. Hydrogeologic conditions that favor high levels of fecal contamination but low levels of arsenic in shallow groundwater should be taken into account during arsenic mitigation throughout South and Southeast Asia.