To improve water quality and construct a landscape lagoon in China, an ecological reconstruction plan for the Qilihai Lagoon (Changli County, Hebei) is proposed. A three-dimensional numerical model (EFDC) was used to study the water renewal capacity in the reconstructed lagoon by using residence time, exposure time and connectivity as timescales. The influences of wind and the depth of the tidal inlet of the lagoon on water renewal capacity were also investigated. The results show that the transport and diffusion processes in the lagoon were strongly influenced by wind and the modification of the tidal inlet. The lagoon under a no wind condition exhibited a low water renewal capacity, especially at the end areas (exposure time, 700–1,000 days). The wind action notably enhanced the water renewal capacity in the lagoon, and the exposure times were all lower than 400 days in the whole region. The optimal inlet depth for the water renewal in the lagoon was predicted to be 4.0 m. The connectivity matrices identified which areas of the domain would be most affected by a pollution source under different conditions. This study examines transport and diffusion processes in a reconstructed lagoon, which could be informative for ecological reconstruction planning.