This study investigates the importance of local vs. spatial factors on bacterial community composition of 35 rock pools at the Baltic Sea coast. The pools were located in five distinct spatial clusters over a total scale of <500 m and differed widely in terms of water chemistry. To determine the fractions of the variance in bacterial community composition (BCC) between rock pools that are explained by local environmental vs. spatial factors, a variance partitioning procedure using partial canonical correspondence analysis was performed. Three environmental variables (salinity, chlorophyll a concentration, and water color) had a significant effect on BCC, irrespective of the spatial location of the pools. Vice versa, there was a significant effect of spatial factors on BCC irrespective of any of the environmental factors included in this study. Hence, the patchy spatial distribution of the pools was partly reflected in the composition of the bacterial communities in the pools, which might be caused by congruent colonization events of adjacent pools, such as simultaneous seaspray inputs or direct exchange of bacteria via connecting rivulets. This study shows that the composition of planktonic bacteria can show provincialism at small spatial scales, which is likely to be caused by environmental conditions as well as historical events.