Denitrification permanently removes nitrate from aquatic ecosystems, so construction of denitrification walls to enhance denitrification activity is often suggested to reduce the nitrate levels from tributary ecosystems. However, little information is available to guide the choice of appropriate organic materials for increasing denitrification rates in the walls. This study investigated how differences in organic substrates originating from litter and organic materials affected denitrification and carbon mineralization rates in riparian sediments. Potential denitrification rates were highest in riparian sediments that contained large quantities of extractable organic carbon (Ext. Org C) and that had high anaerobic carbon mineralization rates, but they were negatively correlated with C:N ratios. Therefore, this research suggested that the both carbon quantity and quality should be considered when assessing the efficiency of organic substrates to remove nitrate from tributary ecosystems.