Natural revegetation alters local hydrodynamic conditions in coastal lagoons. To investigate vertical flow structures in revegetated lagoons, a series of flume experiments are implemented on an immobile bed with Phragmites australis by a certain staggered configuration. Six incident wave heights and five inflow discharges are considered. The experimental results demonstrate that wave dominates turbulent kinetic energy (TKE) distributions under wave-current conditions. Vegetation morphology plays an important role in wave-current-vegetation interactions, which regulates TKE distributions by diminishing wave effects within 70% of water depth especially (0.3 < z/h < 1). The increasing inflow discharge has positive effects on diminishment of wave effects, while the reduction of mean streamwise flow velocity is stable under the present vegetation configuration. Moreover, the practical values of vertical mean flow velocity can be obtained from the empirical equation, which includes wave effects by a quadratic polynomial relationship between the ratio of experimental values to theorical values (U/Up) and the relative wave height H0/h. Furthermore, two relationships are established between the reduction of mean streamwise flow velocity r and z/h, involving a logarithmical relationship in the lower layer (0 < z/h < 0.3), and a cubic polynomial relationship in the upper layer (0.3 < z/h < 0.7).