Our study investigated the impacts of starch botanical origin (tapioca versus wheat starch) and gluten addition on the water distribution and hydrothermal changes of starch in model dough systems compared to their pure starch counterparts. In it, we employed a combination of time-domain nuclear magnetic resonance (TD-NMR), wide angle X-ray diffraction (WAXD), solid state nuclear magnetic resonance (ssNMR) at variable temperature (VT) and differential scanning calorimetry (DSC) measurements. The results showed that at intermediate hydration levels, water ingress into starch granules, increase in glucan chain mobility, and dissociation of double helices (DH) of amylopectin occurred at lower temperatures than crystallite loss of order and melting. The inhibitory effect of gluten on wheat starch hydrothermal changes was explained by a higher water adsorption capacity of gluten compared to starch at this hydration level (50%, wb). However this effect was shown to be influenced by starch botanical origin, tapioca-based systems showing no hindrance effect of gluten on starch-water interaction. The study also provides additional evidence for the sensitivity and detection scales of the different techniques at 50% water content.