Non-point source (NPS) pollution is believed to be one of the major causes of impairment of water bodies. Among NPS pollution, agricultural NPS pollution is considered to be the largest single category resulting in water quality deterioration. Pesticides are some the most ubiquitous of these agricultural NPS pollutants. In this study, a mountainous wetland was selected to investigate the effects of the natural wetland system on the NPS pesticide (atrazine) removal to maintain the surface water quality. The selected wetland receives water from two unnamed creeks, which drain primarily upgradient agricultural lands. Wetland investigation and monitoring were conducted from November 1999 to March 2001. Major storm events and baseline water quality samples were analyzed. Field results indicate that the wetland was able to remove NPS atrazine flushed from the upgradient agricultural lands after the occurrence of storm events. Laboratory aerobic and anaerobic bioreactor experiments were conducted to evaluate the biodegradation of atrazine under the intrinsic conditions of the wetland system. Microbial enumeration was conducted for a quick screen of bacterial activity in the studied wetland. Results from the study suggest that the methanogenesis process was possibly the dominant biodegradation pattern, and atrazine can be degraded under reductive dechlorinating conditions when sufficient intrinsic organic matter was provided. Results from this study can provide us with further knowledge on pesticide removal mechanisms in natural wetlands and evaluate the role of wetlands in controlling pesticide pollutants from stormwater runoff.