The experimentally observed effect of selective deuterium substitution on the open circuit voltage for a blend of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM; Nat. Commun. 2014, 5, 3180) is explored using a 221-atom model of a polymer-wrapped PCBM molecule. The protonic and deuteronic wave functions for the H/D isotopologues of the hexyl side chains are described within a quantum trajectory/electronic structure approach where the dynamics is performed with newly developed nonlinear corrections to the quantum forces, necessary to describe the nuclear wave functions; the classical forces are generated with a density functional tight binding method. The resulting protonic and deuteronic time-dependent wave functions are used to assess the effects of isotopic substitution (deuteration) on the energy gaps relevant to the charge transfer for the donor and acceptor electronic states. While the isotope effect on the electronic energy levels is found negligible, the quantum-induced fluctuations of the energy gap between the charge transfer and charge separated states due to nuclear wave functions may account for experimental trends by promoting charge transfer in P3HT:PCBM and increasing charge recombination on the donor in the deuterium substituted P3HT:PCBM.