Shelter, regarded as a protection against predators and/or nesting site, constitutes one of the basic resources for which organisms compete in the wild. Ponto-Caspian gobies are a good example of a territorial species, which can have negative impact on native species with similar biology due to competitive interactions. Thus, the aim of the present study was to investigate the potential impact of the invasive Ponto-Caspian western tubenose goby Proterorhinus semilunaris on the native stone loach Barbatula barbatula through shelter competition. We used male and female gobies in their reproductive season to test whether they would be more aggressive towards native stone loach, accounting for different light conditions in a limited shelter competition scenario. The results of our study showed that both tested species occupied the shelter mostly during the daylight. Only male goby reduced the shelter occupancy of stone loach despite the fact that interspecific aggressive acts were very rare. It was associated with the nest guarding by male gobies, considering that the study was conducted during their reproductive season. Based on our results, it is possible that, under natural conditions, male tubenose goby would force stone loach to stay away from the shelter, especially in late spring and early summer, when gobies are in reproductive state. This might affect stone loach populations by devoiding them of optimum sites and increasing their exposure to predators.