The environmental transformations of nanomaterials are correlated with their behaviors and ecological risks. The applications of single-layer molybdenum disulfide (SLMoS) have rapidly developed in environmental fields, but the potential transformations and biological effects of SLMoS remain largely unknown. This study revealed that humic acid (HA, over 10 mg/L) induced the scrolling of SLMoS with light irradiation over a 56-day incubation. The colloidal stability of SLMoS increased, and the aggregation ratio decreased from 0.59 ± 0.07 to 0.08 ± 0.01 nm/min after HA hybridization. Besides, compared with pristine SLMoS, the chemical dissolution rate of SLMoS was up to 4.6-fold faster with HA exposure. These results demonstrate that HA affects the environmental fate and transformations of SLMoS. SLMoS-HA possessed a significantly widened direct band gap (2.06 eV) compared with that of SLMoS (1.8 eV). SLMoS acted as an electronic acceptor from HA, resulting in the separation of electron-hole pairs. Consequently, SLMoS-HA exhibited stronger peroxidase-like catalytic activity, which was approximately 2-fold higher than that of SLMoS. Moreover, the morphology and layered structure of SLMoS changed, and the damage SLMoS inflicted on microalgae was significantly reduced. This work provides insights into the behaviors and related biological risks of SLMoS in aqueous environments.