Draft genome sequences of three Shewanella sp. strains are reported. The strains NKUCC01_JLK, NKUCC05_KAH, and NKUCC06_TVS were isolated from freshwater sources in the Ohio River Valley, USA. These genome sequences provide insights into Shewanella adaptation to urban freshwaters and may help to elucidate their roles in biogeochemical cycling.