The environmental behavior and stereoselectivity of the chiral fungicide benalaxyl and its chiral metabolite benalaxyl acid in water, sediment, and water-sediment microcosms were studied. The microcosms were incubated at 25 °C with light or under darkness. The influencing factors such as light and microorganism were investigated. The results showed that benalaxyl had half-lives of >21 days in the microcosm system and that the metabolite benalaxyl acid could exist in the microcosm for >70 days. Benalaxyl was mainly transformed through microbial degradation, and thus sediment microorganisms played a major role in the dissipation of benalaxyl in the aquatic microcosm. The stereoselective behavior of benalaxyl and benalaxyl acid was also investigated. (-)-Benalaxyl was preferentially degraded in the microcosm, resulting in an enrichment of the more toxic enantiomer (+)-benalaxyl, which may cause higher risk to the aquatic system. Moreover, (-)-benalaxyl acid was preferentially formed in the microcosm. The enantioselectivity of the enantiomers in the microcosm should be taken into consideration for an accurate risk assessment.