The water exchange capacity (WEC) in semi-enclosed bays is influenced by various dynamical processes. Among them, the wave effects are important and yet not well-understood. In this study, the Dalian Bay, a typical coastal semi-enclosed bay located in northeastern China, was chosen as an example, and the finite volume community ocean model (FVCOM) coupled with a wave module has been employed to investigate the wave effects on WEC in the Dalian Bay in the summer. The Dalian Bay is composed by three small-sized inner bays, Tianshuitao (TST), Hongtuduizi (HTDZ) and Choushuitao (CST), as well as the central part of the Dalian Bay (CPDB). The model performance has been evaluated comprehensively by comparing a suite of quantitative metrics, procedures and spatiotemporal patterns between the simulated results and time series current and wave measurements. The simulated results well-reproduced the observations, justifying the model’s ability in reproducing the hydrodynamics of the research region. The model results and observation all indicated that the averaged current velocities in the Dalian Bay were increased by about 0.1–0.2 m/s under wave effects during one strong wave event. Especially in the TST, the current velocities were increased most significantly. Moreover, dyed tracer experiments have been conducted to investigate the wave effects on WEC, and half-life time of different subregions of the Dalian Bay were also calculated. The results showed regional differences in wave effects. Overall, the impacts of waves were more significant in the northern part of the Dalian Bay. In the summer, southeast winds prevail, which generate waves in the southeast directions. Facilitated by regional geographical settings, waves could reach the northern part directly, which reduced the dyed tracer concentrations substantially, signifying a stronger WEC. Therefore, waves exerted the greatest impacts on the TST and reduced the local half-life time by about 10–20 days through increasing the efficiency of material transports. And the half-life time of the HTDZ, when considering the wave effects, was reduced by 15 days. However, confined by the twisting coastline, the wave effects on WEC in the CPDB and the CST were not that distinguished compared to the other parts of the bay.