Humic substances (HS) are the most important natural biostimulant of plants. However, the relationship between their structure and biological activity in plants is still not well recognized. The objective of this paper was to assess the influence of molecular fractions of humic acids (HA) (HA < 30 kDa and HA > 30 kDa) on reducing negative effects of drought stress in soybean (Glycine max (L.) Merr.) seedlings of Progres and Nawiko cultivars. Drought stress was induced in laboratory conditions by the addition of polyethylene glycol 6000 (PEG 6000) to make a water potential of −0.5 MPa. HA were extracted according to the International Humic Substances Society procedure, and then were separated into two molecular fractions by membrane filtration. The following physiological and biometric parameters were determined: chlorophyll content, photosynthesis activity, electrical conductivity, fresh and dry mass of overground and roots, and plant length. The enzyme activity and ion contents were also measured. Differences in response to drought stress with the addition of HA < 30 kDa and HA > 30 kDa or not to the Hoagland’s solution were observed among studied cultivars. Drought stress caused a decrease in the most physiological parameters and increase in peroxidase activity in the case of both studied cultivars. However, the results of biometric measurements showed that the Progres cultivar appears to have better tolerance to drought stress. The significant influence of water deficit on most macroelement content in dry matter leaves of both studied cultivars was not observed, while its effect on microelement uptake by soybean plants was concluded. In the case of the Progres cultivar, the results showed a significant decrease in microelement content in the dry matter of leaves, whereas in the leaves of Nawiko cultivar there was a significant increase. The influence of HA > 30 kDa and HA < 30 KDa fractions on physiological features of both studied cultivars was varied. HA > 30 kDa fraction better up-regulated the antioxidant defense system. Unfortunately, no effect of either HA fraction on the macro- and micronutrients uptake system of both studied cultivars was observed.