Removing micropollutants is challenging in part because of their toxicity at low concentrations. A biocatalytic approach could harness the high affinity of enzymes for their substrates to address this challenge. The potential of biocatalysis relative to mature (nonselective ion exchange, selective ion exchange, and whole-cell biological reduction) and emerging (catalysis) perchlorate-removal technologies was evaluated through a quantitative sustainable design framework, and research objectives were prioritized to advance economic and environmental sustainability. In its current undeveloped state, the biocatalytic technology was approximately 1 order of magnitude higher in cost and environmental impact than nonselective ion exchange. Biocatalyst production was highly correlated with cost and impact. Realistic improvement scenarios targeting biocatalyst yield, biocatalyst immobilization for reuse, and elimination of an electron shuttle could reduce total costs to $0.034 m-3 and global warming potential (GWP) to 0.051 kg CO2 eq m-3: roughly 6.5% of cost and 7.3% of GWP of the background from drinking water treatment and competitive with the best performing technology, selective ion exchange. With less stringent perchlorate regulatory limits, ion exchange technologies had increased cost and impact, in contrast to biocatalytic and catalytic technologies. Targeted advances in biocatalysis could provide affordable and sustainable treatment options to protect the public from micropollutants.