Bacterial communities are fundamental components of many processes occurring in aquatic ecosystems, since through microbial activities substantial amount of matter and energy is transferred from a pool of DOC to higher trophic levels. Previous studies highlighted the beneficial effects of diversity on ecosystem functioning, however studies on the resistance and resilience in microbial communities are scarce. Similarly, studies focusing on factors that might improve resistance or resilience of communities such as the influence of refuges are equally missing, although an understanding of the underlying mechanisms could be very useful in the field of conservation management. In this study, chemostat cultures were used to investigate the influence of a spatial and a temporal refuge on bacterioplankton communities’ resistance and resilience measured in terms of functioning and community composition after applying a salinity pulse disturbance. Respiration rate and substrate utilization were used to estimate bacterial functioning while community composition was determined by using T-RFLP. The perturbation was found to affect bacterial functioning and community composition. Moreover our findings indicate that the resistance and resilience measured in terms of bacterial functioning and community composition were significantly influenced by the provision of refuges.