Vegetation patches increase the pressure gradient of local channels and can create an uneven pressure distribution at the water–sediment interface, thereby driving hyporheic exchange. However, this process has rarely been discussed. We investigated the spatiotemporal characteristics of hyporheic exchange under the influence of multiple factors. A bidirectional coupling model of the overlying water and sediment with an emergent vegetation patch was adopted. The results show that hyporheic exchange driven by vegetation patches are spatially heterogeneous. The active area of hyporheic exchange was concentrated directly below the vegetation patch. A finger flow was formed at the edge of the active hyporheic exchange zone as the exchange took place. Furthermore, intermittent downward solute transport path (IDSTP) was formed downstream of the vegetation patch, and the exchange rate was one order of magnitude smaller than that of the hyporheic exchange active zone. Hyporheic exchange occurred at the stem and patch scales when the vegetation density was relatively high. There was a logarithmic relationship between the hyporheic exchange flux and sediment permeability, and a power function relationship existed between the hyporheic exchange flux and Reynolds number. The active area of hyporheic exchange will help predict pollutant transport and understand vegetation's nutrient absorption process. IDSTP will provide references for vegetation patch expansion.