Agricultural nonpoint pollution has been recognized as a primary source of nutrients and pesticides that contaminate surface water and groundwater. Reactive materials have great potential to remove nutrients and pesticides from agricultural drainage water. In this study, we investigated the reactive transport and removal of coexisting nitrate, phosphate, and three pesticides (tricyclazole, isoprothiolane, and malathion) by iron filings and natural ore limestone through column experiments under saturated flow conditions. Breakthrough results showed that 45.0% and 35.8% of nitrate were removed by iron filings and limestone during transport, with average removal capacities of 2670 mg/kg and 1400 mg/kg, respectively. The removal of nitrate was mainly due to microbial denitrification especially after 131–154 pore volumes (≈30 d), whereas reduction to ammonia dominated nitrate removal in iron filings during early phase (i.e., <21.7 d). The results showed that 68.2% and 17.6% of phosphate were removed by iron filings and limestone, with average removal capacities of 416.1 mg/kg and 155.2 mg/kg, respectively. Mineral surface analyses using X-ray diffraction (XRD) and scanning electron microscope (SEM) coupled with energy-dispersive X-ray analysis (EDX) suggested that ligand exchange, chemical precipitation, and electrostatic attraction were responsible for phosphate removal. Chemical sorption was the main mechanism that caused removals of 91.6–100% of malathion and ≈27% of isoprothiolane in iron filings and limestone. However, only 22.0% and 1.1% of tricycalzole were removed by iron filings and limestone, respectively, suggesting that the removal might be relevant to the nonpolarity of tricyclazole. This study demonstrates the great potential of industrial wastes for concurrent removal of nutrients and pesticides under flow conditions.