Iron is known to be significantly related with phosphorus runoff from watersheds, yet there is a lack of knowledge regarding this phenomenon from the viewpoint of the iron load. Therefore, we conducted a 17-month investigation on the behavior and annual mass balance of iron and phosphorus in a paddy field area where sediment of iron oxides accumulated. Most iron and phosphorus were present as particulate matter, with low concentrations of dissolved ions. Annual net-outflow loads of iron and phosphorus were 108.6 kg/ha (irrigation period: 37.3 kg/ha; non-irrigation period: 71.3 kg/ha) and 3.40 kg/ha (irrigation period: 1.49 kg/ha; non-irrigation period: 1.91 kg/ha), respectively. A possible reason that no phosphorus purification was observed at the study site despite the sufficient amount of iron, which has adsorption capacity for phosphorus, is sediment detachment and runoff due to water flow in the drainage canal. This suggests that management of phosphorus-rich sediment is an essential factor for controlling the outflow of phosphorus.