Hydrogels are great systems for bioactive agent encapsulation and delivery. In this study, polysaccharide blended whey protein isolate (WPI) based hydrogels were loaded with black carrot (Daucus carota) concentrate (BC) and in vitro gastrointestinal release measurements were performed. Prior to 6 h digestion in simulated intestinal fluid (SIF), all hydrogels were exposed to simulated gastric fluid (SGF) for 2 h. Pectin (PC), gum tragacanth (GT) and xanthan gum (XG) were the polysaccharides used with WPI to manipulate the release behavior. Physico-chemical changes of the hydrogels throughout the digestion were evaluated by Fourier transform infrared (FTIR) spectroscopy and nuclear magnetic resonance (NMR) relaxometry measurements. Each polysaccharide induced different physico-chemical interactions within the hydrogels due to their distinct structural characteristics. Polysaccharide blending to hydrogels also retarded the release rates in all samples in SIF (p < 0.05). Moreover, microstructural differences between hydrogels were evaluated by scanning electron microscope (SEM) images.