Journal article ; Engineered remediation technologies such as denitrifying bioreactors target single contaminants along a nutrient transfer continuum. However, mixed contaminant discharges to a water body are more common from agricultural systems. Indeed, evidence presented herein indicates that pollution swapping within denitrifying bioreactor systems adds to such deleterious discharges. The current paper proposes a more holistic approach to contaminant remediation on farms, moving from the use of denitrifying bioreactors to the concept of a permeable reactive interceptor (PRI). Besides management changes, a PRI should contain additional remediation cells for specific contaminants in the form of solutes, particles or gases. Balance equations and case studies representing different geographic areas are presented and used to create weighting factors. Results showed that national legislation with respect to water and gaseous emissions will inform the eventual PRI design. As it will be expensive to monitor a system continuously in a holistic manner, it is suggested that developments in the field of molecular microbial ecology are essential to provide further insight in terms of element dynamics and the environmental controls on biotransformation and retention processes within PRIs. In turn, microbial and molecular fingerprinting could be used as an in-situ cost-effective tool to assess nutrient and gas balances during the operational phases of a PRI. ; Department of Agriculture, Food and the Marine - Research Stimulus Fund (RSF 07 525) ; peer-reviewed