Vegetation plays a key role in trapping sediments and further controlling pollutants. However, few studies were conducted to clarify the erosion and deposition laws of sediments and the influence factors caused by vegetation patch properties, which is not conducive to the revelation of riverbank protection and erosion prevention. Therefore, this study investigated the change in scouring and deposition characteristics around submerged vegetation patches of nine kinds of typical configurations and their influencing factors. Vegetation patches were assembled from three vegetation densities (G/d = 0.83, 1.3, and 1.77, representing dense, medium, and sparse, respectively), and three vegetation patch thicknesses (dn = 170, 400, and 630, representing narrow, usual, and wide, respectively), to measure vegetation patch property influences. Flow velocity, scouring, and deposition characteristics under nine patches were determined by a hydraulic flume experiment, three-dimensional acoustic Doppler velocimetry (ADV), and three-dimensional laser scanner, and then ten geometry and morphology indices were measured and calculated based on the results of laser scanning. Results showed that both vegetation patch density and thickness were positively related to the turbulence kinetic energy (TKE) above the vegetation canopy, and only vegetation patch density was negatively related to the flow velocity above the vegetation canopy. The relation between the product of density and vegetation patch thickness and erosion area in planform (EA) showed a power function (R2 = 0.644). Both density and vegetation patch thickness determined the scouring degree, but deposition location and amount did not rely on each one simply. On average, medium density showed the smallest maximum erosion length (MEL), EA, deposition area in planform (DA), and average deposition length (ADL) and a minimum of the above parameters also occurred at narrow vegetation patch thickness. The shape factor of the erosion volume (SFEV), the shape factor of the deposition volume (SFDV), ADL, and MEL of medium density and narrow thickness vegetation patch (G/d = 1.3, dn = 170) were significantly smaller than that of other types of patches. DA and equivalent prismatic erosion depth on the erosion area (EPED) were significantly linearly related (R2 = 0.766). Consequently, most sediment was deposited close to the vegetation patch edge. It is suggested that vegetation patch thickness and density should be given to control sediment transport. In particular, natural vegetation growth changes vegetation patch density and then alters vegetation patch thickness. Management and repair need to be first considered. The results of this study shed light on riparian zone recovery and vegetation filter strip mechanism.