BACKGROUND: With increasing public awareness to environment-friendly agriculture, many efforts have been run to develop organic farming technologies in Korea as of late 90s. The objective of this study was to investigate the effects of different organic farming practices on soil chemical properties and water quality in paddy fields. METHODS AND RESULTS: Total nitrogen (TN) and total phosphorus (TP) were monitored for a two-year period (2006 to 2007) from the study organic paddy fields located in Wan-ju, Jeonbuk Province in Korea. TN and TP of organic paddy water were gradually increased for 2~3 weeks after organic manure application and then gradually decreased afterward. The overall variation of TP in the paddy fields was much greater than that of TN. The phosphorus content in organic paddy field appeared to increase with the organic farming period. CONCLUSION(s): This indicates that long-term organic farming is likely to cause phosphorus accumulation in soils and increase vulnerability to rainfall runoff. Thus, appropriate phosphorus management needs to be implemented, particularly, to reduce excessive phosphorus supply owing to nitrogen-based determination of organic manure application amount.