Monitoring of a well-defined septic system groundwater plume and groundwater discharging to two urban streams located in southern Ontario, Canada, provided evidence of natural attenuation of background low level (ng/L) perchlorate (ClO4−) under denitrifying conditions in the field. The septic system site at Long Point contains ClO4− from a mix of waste water, atmospheric deposition, and periodic use of fireworks, while the nitrate plume indicates active denitrification. Plume nitrate (NO3−-N) concentrations of up to 103 mg/L declined with depth and downgradient of the tile bed due to denitrification and anammox activity, and the plume was almost completely denitrified beyond 35 m from the tile bed. The ClO4− natural attenuation occurs at the site only when NO3−-N concentrations are <0.3 mg/L, after which ClO4− concentrations decline abruptly from 187 ± 202 to 11 ± 15 ng/L. A similar pattern between NO3−-N and ClO4− was found in groundwater discharging to the two urban streams. These findings suggest that natural attenuation (i.e., biodegradation) of ClO4− may be commonplace in denitrified aquifers with appropriate electron donors present, and thus, should be considered as a remediation option for ClO4− contaminated groundwater.