According to the theory of island biogeography, species richness in island-like systems is determined by ecosystem size and isolation. However, there is only very little information about how this theory applies to microorganisms. The aim of this study was to examine the effects of local physicochemical variables, land use and geographical factors on diatom species richness and community composition in 50 boreal springs in Finland, and to test for species-area and species- isolation relationships. There were nonsignificant relationships between species richness and spring area and isolation. The best approximating generalized linear model suggested that variation in species richness was related to several local resource and stress factors such as water conductivity, pH, colour, temperature and nutrient concentrations. Based on Mantel tests, diatom community similarity was significantly correlated with environmental distance, but not with geographical distance. Analysis of similarities further showed that community compositions did not differ significantly between ecoregions. These results suggest that spatial factors are of minor importance for spring diatoms compared with environmental filtering. Patterns in spring diatoms do not concur with the theory of island biogeography as we found no support for species-area or species-isolation relationships. At these spatial scales, dispersal limitation does not seem to influence diatom communities.