Geomorphic conditions and the resulting turbulence are significant factors that influence coastal lagoonal environments. In this study, a shallow-water hydrodynamic transport model was employed to investigate turbulence related to geomorphic features in a large shallow lagoon (Xiaohai Lagoon) in China and to explore the effects these features have on horizontal mixing and the dissipation of tidal energy within the lagoon. At various tidal stages, the vorticity distribution revealed the presence of large-scale turbulent structures associated with the local geomorphic features found in the downstream part of Xiaohai Lagoon, which enhanced flow shear in the affected area and governed local mixing. Increased tidal range enhanced the horizontal mixing flux in the upstream part of the lagoon during spring-neap cycles. In contrast, the mixing flux in the downstream region declined during spring tides and increased during neap tides due to phase differences between tidal flow processes and tracer concentration. In addition, tidal energy dissipation was most concentrated in the vicinity of the local geomorphic features. The rate of dissipation from the inlet to the upstream end of the deep groove accounted for 99.6% of the total in Xiaohai Lagoon, resulting in a loss of 72% of the tidal range in the upstream region, which substantially limited the upstream tidal prism and water mixing. This study suggests that turbulent mixing and energy dissipation associated with local geomorphic features are important mechanisms governing water exchange and environmental heterogeneity in lagoons and should be considered when formulating management and optimization strategies for coastal lagoons.