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Reclaimed water plays an important role in maintaining urban aquatic ecosystems, especially in areas with water shortages. However, there is little information on water quality dynamics and its driving mechanism in reclaimed water bodies. The simulated experiments were conducted to investigate the effect of flow exchange on water quality dynamics and soil microbial diversity for 100% reclaimed water and mixed water (50% reclaimed and 50% stream water), and the exchange periods ranged from 2 to 40 days. The results showed that the degradation coefficients (K) of CODMn and NH3–N were 0.015 d−1 and 0.001 d−1 for the mixed water, while their K values were negative for the reclaimed water. The flow exchange had little effect on water quality dynamics for the mixed water, which may be attributed to the relatively low concentration of TP in this reclaimed water. A small or great exchange period led to a relatively high fluctuation in K during the experimental period and corresponded to a worse soil microbial diversity. These results indicate that it is not recommended to fill an isolated urban lake with 100% reclaimed water and that a suitable flow exchange period of 5~10 days could help self-purify the water quality.