Polar and apolar moieties of humic acids are spatially separated forming domains of different polarity. In this work, we tested the procedures to crosslink functional groups in polar domains of humic acids by using carbodiimide coupling and analyzed to which extent influenced the modification their hydration properties and stability. For this reason, we prepared eight derivatives of lignite humic acids using either water-soluble N-Ethyl-N′-(3-dimethylaminopropyl)carbodiimide (EDC) or water-insoluble N,N′-dicyclohexylcarbodiimide (DCC) under various conditions. Characterization of prepared derivatives showed that both methods lead to formation of crosslinked humic structures. Using of EDC resulted in lower degree of crosslinking, but better hydration properties. Higher moisture uptake and water holding capacity were observed in humic acids, which were pre-wetted prior to crosslinking for at least 24 h. Although the EDC derivatives of humic acids contained only between 60 and 85% of original free carboxylic groups, they showed similar moisture uptake as parental humic acids by equilibration at relative humidities of both 94% and 76%. Under water-saturated conditions, the EDC derivatives showed faster swelling kinetics and reached almost the same water holding capacity as the original sample after 18 days. However, both the EDC and DCC derivatives began to degrade already after 3–9 days during swelling tests, which subsequently decreased their hydration. The results suggested that water holding capacity, swelling kinetics and moisture uptake of humic acids were not influenced significantly by the amount of polar groups, but also by their spatial arrangement and distribution.