This study tested the contaminant removal effect under the conditions of substrate combination, packing arrangement, and hydraulic loading under four substrates (gravel, zeolite, ceramsite and vermiculite) as part of an attempt to improve the purification capacity of ecological filter dams. The results showed that the gravel and ceramsite group had the superior COD removal efficiency, whereas the best removal efficiencies of NH+4-N and TP were achieved by the gravel and zeolite group. It was also found that uniform mixing mode could most effectively improve the removal of COD, but the best removal efficiencies of NH+4-N and TP were found in the gravel in former and zeolite in behind mode. With the increase of hydraulic loading, the removal rates of COD and TP in three mixing modes were gradually decreased, and NH+4-N removal behaved decrease in uniform mixing mode, but increased first and then decreased in two-layer mixing modes.