Pesticide residues in riparian zones have attracted much attention in recent decades. Their accumulations potentially deteriorate microbial activity and disturb nitrogen cycle in riparian sediments. In this study, the short-term effects of chlorothalonil (CTN, a common pesticide) on microbial denitrification were explored in riparian sediments at three levels (5, 10 and 25 mg kg(-1)). No significant differences were observed between control and 5 mg kg(-1) treatment; however, CTN in 10 and 25 mg kg(-1) treatments deteriorated sediment health condition and microbial activity. High concentrations of CTN also significantly decreased denitrification rates ((15) N pairing method) by 37-62%, but increased N2O emission in riparian sediments by 100-285%. Our data further revealed that CTN inhibited key enzyme activities responsible for microbial metabolism, and declined electron donor (NADH) and energy source (ATP) levels during denitrification. Key denitrifying enzyme activities were also suppressed by CTN, which explained the declined denitrification process and the elevated N2O emission. Additionally, high-throughput sequencing and quantitative-PCR analysis showed that CTN didn't remarkably change microbial community structures and denitrifying gene abundances after short-term exposure. Overall, this study highlights that riparian pesticides could impact nitrogen cycle of the interface between terrestrial and aquatic ecosystems, potentially accelerating water pollution and global climate change.