The capture of colloidal fine suspended particles by vegetation plays an important role in water quality of the shallow aquatic system under rainfall. Quantifying impact of rainfall intensity and vegetation condition on this process remains poorly characterized. In this study, the colloidal particle capture rates under three rainfall intensities, four vegetation densities and with submerged or emergent vegetation were investigated in different travel distance in a laboratory flume. Considering vegetation as porous media, non-Darcy's law with rainfall as a source term, was coupled with colloid first-order deposition model, to simulate the particle concentration changes with time, determining the particle deposition rate coefficient (kd), representing capture rate. We found that the kd increased linearly with rainfall intensity; but increased and then decreased with vegetation density, suggesting the existence of optimum vegetation density. The kd of submerged vegetation is slightly higher than emergent vegetation. The single collector efficiency (η) showed the same trend as kd, suggesting colloid filtration theory well explained the impact of rainfall intensity and vegetation condition. Flow hydrodynamic enhanced the kd trend, e.g., the theoretical strongest flow eddy structure represented in the optimum vegetation density. This study is helpful for the design of wetland under rainfall, to remove colloidal suspended particles and the hazardous material, for the protection of the downstream water quality.