Spectral hole-burning spectroscopy has been applied to proton conducting SrZrO3:Y3+ Single crystals. Transient and persistent hole-burning were observed in EU(3+) and Pr3+ doped SrZrO3:Y3+ crystals, respectively. It is shown that holes can be burned by the optical pumping of the nuclear quadrupole levels of EU(3+). Since the spectral hole in Pr3+ doped crystals is observed only in H2O- or D2O-annealed samples, the hole-burning is caused by light-induced H+ or D+ motion which leads to persistent changes in the local crystal fields around the Pr3+ ions. The barrier height of proton (deuteron) tunneling transport is estimated in the Pr3+ doped system. The relationship between the long range proton conduction at high temperature and the local proton dynamics at low temperature is discussed.