Proton dynamic in Y-doped BaZrO3 derivatives were studied by classical Molecular Dynamics calculations, investigating different dopant environments within a Pm-3m cubic framework. Single and double substitutions of zirconium by doping yttrium atoms were considered. The presence of yttrium induces variations in the surrounding oxygen sites, according to their local geometrical arrangement. The differences of such distinct oxygen sites become evident when protons interact with them and upon temperature changes. So, different proton transfer pathways, having different energy barriers, characterize topologically differing oxygen sites. The experimental proton-hopping activation energy is reproduced only in those structures where two yttrium atoms form an Y-O-Y arrangement, which also acts as multilevel protonic traps. Protonic conduction in these materials could be improved avoiding such yttrium clustering hence preventing the formation of the protonic traps.