The potential widespread applications in water processing have rendered the necessity for investigations of the fate and hazard of molybdenum disulfide (MoS2) nanosheets. Herein, it was found that humic acid (HA) had better performances toward stabilizing pure 2H phase MoS2 and chemical-exfoliated MoS2 (ce-MoS2) in electrolyte solutions than fulvic acid (FA), and molecular weight (MW)-dependent manners were disclosed due to steric repulsions. Compared with darkness, the extent to which the aggregation and sedimentation of ce-MoS2 facilitated by visible light irradiation was greater in the presence of HA and FA fractions, likely due to the introduction of stronger plasmonic dipole-dipole interaction and Van der Waals attraction forces. HA-triggered structural disintegration of nanosheets was performed after irradiation and it was observed to be more significant with the increase in MWs, whereas the MW-dependent dissolution of MoS2 caused by FA was much quicker than that by HA owing to the higher generation of singlet oxygen. Moreover, FA lowered the bioavailability of MoS2 and relieved its toxicity to zebrafish more effectively than HA. Our findings boost the insights into the effects of organic molecules on the fates and hazards of MoS2, providing guidance for the MoS2-based nanotechnological development on environment.