We present a theoretical analysis of the electron spin echo envelope modulation (ESEEM) spectra of polarons in semiconducting π-conjugated polymers. We show that the contact hyperfine coupling and the dipolar interaction between the polaron and the proton spins give rise to different features in the ESEEM spectra. Our theory enables direct selective probe of different groups of nuclear spins, which affect the polaron spin dynamics. Namely, we demonstrate how the signal from the distant protons (coupled to the polaron spin via dipolar interactions) can be distinguished from the signal coming from the protons residing on the polaron site (coupled to the polaron spin via contact hyperfine interaction). We propose a method for directly probing the contact hyperfine interaction, that would enable detailed study of the polaron orbital state and its immediate environment. We also analyze the decay of the spin echo modulation, and its connection to the polaron transport.