The influent type of organic matter (dissolved or particulate) on the characteristics of two subsurface wastewater infiltration systems (SWISs) was investigated. One of the SWISs was fed with dissolved organic matter (glucose, assumed to be readily biodegradable) and the other with particulate organic matter (starch, assumed to be slowly biodegradable). Results showed that both biofilm growth and particle accumulation in substrate could reduce the effective porosity and infiltration rate of SWIS, especially for the high organic matter concentration wastewater. The reduction in effective porosity and infiltration rate was primarily caused by organic particle accumulation. The contribution of the accumulated organic particle to the process of clogging was greater than that of biofilm growth and the clogging mainly occurred in the upper layer in starch-fed systems. The SWISs fed with glucose were not clogged till the end of experiments. The hydraulic retention time (HRT) increased with time in start-up period and was almost invariable after mature in glucose-fed systems; in starch-fed systems, clogging of substrate prolonged the HRT. The two identical experimental SWISs were almost equal efficiencies for the removal of chemical oxygen demand (COD). The removal efficiencies of COD were not influenced by clogging under the experimental conditions. Ammonia N removal efficiency was higher in glucose-fed systems than that in starch-fed systems.