Solid-state qubits from paramagnetic point defects in solids are promising platforms to realize quantum networks and novel nanoscale sensors. Recent advances in materials engineering make it possible to create proximate qubits in solids that might interact with each other, leading to electron spin or charge fluctuation. Here we develop a method to calculate the tunneling-mediated charge diffusion between point defects from first principles and apply it to nitrogen-vacancy (NV) qubits in diamond. The calculated tunneling rates are in quantitative agreement with previous experimental data. Our results suggest that proximate neutral and negatively charged NV defect pairs can form a NV-NV molecule. A tunneling-mediated model for the source of decoherence of the near-surface NV qubits is developed based on our findings on the interacting qubits in diamond.