For shortage of water source, reclaimed wastewater is commonly used as source water for various landscaping lakes in Peking, China and many other cities. Commonly, ecological restoration was conducted for those lakes to improve the transparency and control the algae outbreak, whereas, the bacterial water quality was rarely assessed. To investigate the bacterial water quality in reclaimed water lakes after ecosystem restoration, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), 16S rRNA gene clone library analysis were used for bacterial diversity investigation; and culture techniques and quantitative polymerase chain reaction (qPCR) analysis were used for bacterial abundance investigation. Obvious variations in aquatic bacterial diversity were observed between the lake and the source water, indicating that the bacterial community construction varied after aquatic eco-restoration. The bacterial composition was clustered by depth rather than by individual site. A higher diversity was observed in bottom water than in surface water. Proteobacteria and Bacteroidetes were proven to be the dominant components of the bacterial population in the surface water of the reclaimed lake. The most dominant phylotypes in surface water were closely related to Arcocella aquatica, Cupriavidus taiwanensis, and Flavobacterium limicola. These dominant bacteria may also be related to the improvement in water quality. Overall, the results are helpful in understanding further the function of these bacteria in reclaimed water and in screening for useful bacterial strains.