3,4-Methylenedioxypyrovalerone (MDPV) is an emerging, chiral, new psychoactive substance belonging to the synthetic cathinones group that has been frequently detected in wastewater effluents and aquatic environments. However, the knowledge of its enantioselective occurrence and toxicity toward aquatic organisms is scarce. The aim of this work was to develop an enantioselective liquid chromatography (LC) method to monitor the enantiomers of MDPV in environmental and ecotoxicological assays. For that, different chiral columns and mobile phases in both normal and reversed elution modes were attempted. The optimized conditions were achieved using a Daicel® 3 μm—CHIRALPAK® IF-3 column with 5 mM of ammonium bicarbonate (NH4HCO3, pH 8.8) in ultra-pure water (UPW) and acetonitrile (ACN) (10:90, v/v) as a mobile phase, at a flow rate of 0.3 mL min−1. This condition was applied to monitor the racemate and the single enantiomers of MDPV in culture medium collected from ecotoxicity experiments. Racemization was observed for MDPV enantiomers (in individual exposure). The enantiomeric ratio (e.r.) of (S)-MDPV changed from an initial e.r. of 96.4/3.6 to 78.0/22.0 and for the (R)-enantiomer, the e.r changed from 15.6/84.4 to 28.3/71.7). These data highlight the importance of enantioselective monitoring of culture media in toxicity assays that involve chiral substances, since racemization can occur and lead to inaccuracy in the toxicity evaluation. Nevertheless, it is also important to stress that racemization may occur during storage conditions or sample procedures. Therefore, the enantioselective methodology is of utmost importance to warrant the quality of the results in enantioselective ecotoxicological studies.