Synthetic pyrethroids are widely used insecticides, and contamination of surface aquatic ecosystems by pyrethroid residues from runoff is of particular concern because of potential aquatic toxicity. Pyrethroids also are chiral compounds consisting of multiple stereoisomers. In the present study, we evaluated the diastereomer and enantiomer selectivity of cis-bifenthrin (cis-BF) and permethrin (PM) in their aquatic toxicity and biodegradation. The 1R-cis enantiomer was the only enantiomer in cis-BF showing toxicity against Ceriodaphnia dubia. Incubation with pesticide-degrading bacteria showed that the trans diastereomer of PM was selectively degraded over the cis diastereomer, whereas the 1S-cis enantiomer in cis-BF or cis-PM was preferentially degraded over the corresponding 1R-cis enantiomer. The enantioselectivity was significantly greater for cis-PM than for cis-BF and also varied among different strains of bacteria. Isomer selectivity may be a common phenomenon in both aquatic toxicity and biodegradation of pyrethroids, and this should be considered when assessing ecotoxicological risks of these compounds in sensitive ecosystems.