This study aimed to evaluate the influence of indirect-plasma-treated water (IPTW) in the preparation of hydrogels. Three commonly used natural, biodegradable polymers with the ability to form gels were selected: gelatin, carrageenan, and sodium alginate. The pH, gelling temperature, texture profile, swelling degree, and color of hydrogels were evaluated, and the polymers were subjected to Fourier-transform infrared (FTIR) spectroscopy. The morphology of the hydrogels was investigated using Scanning Electron Microscopy (SEM). Additionally, the physiochemical properties of the water media, which were distilled water (DW) and IPTW, were analyzed. The results indicated that the gels prepared using IPTW were characterized by a lower pH, higher hardness and lower gelation temperature. After 48 h of swelling ratio (SR) testing, gelatin and alginate hydrogels made with IPTW were characterized by lower SR, while an inverse relationship was found in the case of SR of carrageenan gels. The FTIR analysis confirmed changes in the water binding ability. The use of IPTW also significantly affected the microstructure of the tested materials. A statistically significant change in the color of IPTW gel samples was also noted. The results showed that IPTW induces physicochemical changes in hydrogels, which can lead to the enhancement of their practical applications.