We have used a combination of optical absorption and electrical conductivity measurements to study the effect of the main donor on small polarons in rutile TiO2 single crystals rendered n-type conductive by hydrogenation or doping with Nb. The electrical conductivity measured at 295 K for hydrogenated samples shows a clear correlation with the interstitial hydrogen (Hi) concentration, which is consistent with reports that Hi is the main shallow donor in rutile TiO2. Conductive samples exhibit two distinct optical absorption bands in the IR spectral region, at ω1 = 6500 cm−1 (∼0.8 eV) and ω2 = 3100 cm−1 (∼0.4 eV), which are present in both hydrogen-rich and Nb-doped samples. The intensities of the absorption bands are proportional to the electrical conductivity, and they exhibit an Arrhenius-like temperature dependence for temperatures between 25–50 K and 50–100 K for H-doped and Nb-doped samples, respectively. The thermal activation energies (EAs) for the absorption bands depend strongly on the main donor: ω2 exhibits EA(H) and EA(Nb) of ∼4 and ∼10 meV, respectively, whereas ω1 shows EA(H) and EA(Nb) of ∼1 and ∼2 meV, respectively. The combination of temperature-dependent data for the optical absorption bands and interstitial deuterium (Di)-small polaron vibrational lines support a model where the thermal activation is associated with the reconfiguration of small polarons involving Ti sites far away from the donor. The thermal activation of the optical absorption bands gives us insight into the dynamics of donor-dependent small polaron reconfiguration in rutile TiO2.