Information about estuarine mixing and its control of sediment transport is crucial to elucidating the dynamics and evolution of estuaries. Here, the microtidal and funnel-shaped Zhenhai Estuary, located in the southwestern Pearl River Delta of China, is used to investigate the characteristics and mechanisms of water mixing and sediment transport based on observations from three spring tides. The results reveal that the studied estuary remains well mixed during spring tides from 2013–2022 despite its microtidal regime. Tidal stirring, which is enhanced by tidal energy convergence and benefits from the funnel-shaped geometry and shallow bathymetry, favors vertical mixing, contributing to the formation of strong mixing in the estuary. Due to the well-mixed regime, sediment transport in the estuary is dominated by the advective term, followed by a moderate tidal pumping term and minor estuarine circulation term. Accordingly, sediments within the estuary tend to be transported landward owing to the regulation of the funnel-shaped geometry, and a gradual but slow infilling trend is predictable. This paper deepens our understanding of hydrodynamics and sediment transport in microtidal estuaries.