Increases in the use and application of pyrethroid insecticides have resulted in concern regarding potential effects on aquatic ecosystems. Methods for the detection of pyrethroids in receiving waters are required to monitor environmental levels of these insecticides. One method employed for the identification of causes of toxicity in aquatic samples is the toxicity identification evaluation (TIE); however, current TIE protocols do not include specific methods for pyrethroid detection. Recent work identified carboxylesterase treatment as a useful method for removing/detecting pyrethroid-associated toxicity. The present study has extended this earlier work and examined the ability of carboxylesterase activity to remove permethrin- and bifenthrin-associated toxicity to Ceriodaphnia dubia and Hyalella azteca in a variety of matrices, including laboratory water, Sacramento River (CA, USA) water, and Salinas River (CA, USA) interstitial water. Esterase activity successfully removed 1,000 ng/L of permethrin-associated toxicity and 600 ng/L of bifenthrin-associated toxicity to C. dubia in Sacramento River water. In interstitial water, 200 ng/L of permethrin-associated toxicity and 60 ng/L of bifenthrin-associated toxicity to H. azteca were removed. The selectivity of the method was validated using heat-inactivated enzyme and bovine serum albumin, demonstrating that catalytically active esterase is required. Further studies showed that the enzyme is not significantly inhibited by metals. Matrix effects on esterase activity were examined with municipal effluent and seawater in addition to the matrices discussed above. Results confirmed that the esterase retains catalytic function in a diverse array of matrices, suggesting that this technique can be adapted to a variety of aquatic samples. These data demonstrate the utility of carboxylesterase treatment as a viable step to detect the presence of pyrethroids in receiving waters.