Urban flooding can dramatically affect the local microbial landscape and increase the risk of waterborne infection in flooded areas. Hurricane Harvey, the most destructive hurricane since Katrina in 2005, damaged more than 100000 homes in Houston and flooded numerous wastewater treatment plants. Here we surveyed microbial communities in floodwater inside and outside residences, bayou water, and residual bayou sediment collected immediately postflood. Levels of Escherichia coli, a fecal indicator organism, were elevated in bayou water samples as compared to historical levels, as were relative abundances of key indicator genes of anthropogenic sources of antibiotic resistance (sul1/16S rRNA and intI1/16S rRNA) based on 6 month postflood monitoring. Quantitative polymerase chain reaction measurements showed that gene markers corresponding to putative pathogenic bacteria were more abundant in indoor floodwater than in street floodwater and bayou water. Higher abundances of 16S rRNA and sul1 genes were also observed in indoor stagnant waters. Sediments mobilized by floodwater exhibited an increased abundance of putative pathogens postflood in both residential areas and public parks. Overall, this study demonstrates that extreme flooding can increase the level of exposure to pathogens and associated risks.