Natural zeolite and rice straw have been widely used for removing nitrogen (N) from wastewater due to their different N removal mechanisms. In this study, the N removal performances of three substrate systems composed of zeolite (Z), rice straw (R) and their combination (ZR) were assessed for decontaminating farmland runoff characterized by high loads of ammonium - N or nitrate - N besides of a low carbon content. The N-cycling functional genes were also investigated. The results showed that ZR achieved significantly higher ammonium (48.9%–77.7%) and TN (39.7%–65.9%) removal rates than Z and R ( P < 0.05). ZR also exhibited the highest removal rates of nitrate (67.6%–82.7%) and TN (45.5%–62.1%) in nitrate wastewater treatment. The abundances of 16S rRNA and denitrifying genes (including nirK , nirS , narG and napA ) were significantly enhanced in ZR, which partly explained the higher N removal in the ZR than in the Z and R systems. These findings suggest that it is feasible to combine rice straw with zeolite as a substrate of drainage ditches for considerable N removal enhancement in the control of agricultural runoff. • ZR showed the highest nitrogen (N) removal rate when both NH 4 + -N and NO 3 − -N wastewaters were treated. • TN and NO 3 − -N removal in Z was limited by insufficient denitrification due to low organic carbon source. • The combination of zeolite and rice straw significantly increased the abundances of 16S rRNA and denitrifying genes.