As a result of pollution in the present water sources, cities have been forced to utilize cleaner water sources. There are few reports regarding the potential shift of bacterial community structure driven by water source switching, especially that of corrosion-related bacteria. Three types of finished water were used for simulation, the polluted source water from the Qiantang and Dongtiaoxi Rivers (China) was replaced by cleaner water from Qiandao Lake (China). Here, we discussed the transition effects through three simulated reactors. The bacterial characteristics were identified using the high-throughput sequencing and heterotrophic plate count method. It was observed that the level of culturable bacteria declined by 2–3 orders of magnitude after water source switching. The bacterial community released from the pipeline reactor was significantly different under different finished water, and it exhibited large variation at the genus level. Porphyrobacter (58.2%) and Phreatobacter (14.5%) clearly replaced Novosphingobium, Aquabacterium, and Cupriavidus as new dominant genera in system A, which could be attributed to the lower carbon and nitrogen content of the new water source. Although corrosion-inhibiting bacteria decreased after switching, they still maintained dominant in three reactors (6.6%, 15.9%, and 19.7%). Furthermore, potential opportunistic pathogens such as Sphingomonas were detected. Our study shows that after transition to a high quality water source, the total culturable bacteria released was in a downtrend, which leads to a great reduction in the risk of bacterial leakage in the produced drinking water.