When flooding occurs, harmful microbes from sewage and livestock waste can contaminate private well water, and microbial community dynamics are impacted by aquifer type. Purging wells may remove contaminated water, but it is not understood how flooding, purging, and aquifer type affects microbial communities. For this study, we tested wells in Chesapeake, VA after Hurricane Mathhew and results indicate: (1) Flooded wells, regardless of aquifer type showed signs of microbial contamination. (2) A well outside the mapped flood zone had microbial contamination, suggesting flood maps may not accurately identify risk areas. (3) Purging did not significantly impact the microbial community. (4) The type of aquifer had the greatest impact on microbial community structure. These findings show that flooding can affect wells in variable aquifer types (even confined, deep aquifers), and that remediation plans should consider the aquifer and local conditions.