We sampled 100 small lakes in Finland for bacterio‐, phyto‐, and zooplankton. The lakes were located in five drainage systems, 20 lakes for each system. We tested two main predictions: that the correlation between community similarity and geographical distance (spatial distance decay) is stronger at the across‐drainage than at the within‐drainage system scale, and that spatial distance decay is strongest for zooplankton and weakest for bacteria. We used a combination of direct ordination, multivariate statistical tests, and distance‐based approaches to examine spatial patterns in our data. Our analyses confirmed both of our predictions. Spatial distance decay was scale‐dependent; communities were overall weakly spatially structured within the drainage systems, yet distance decay was significant for all planktonic groups across drainage systems. Spatial distance decay was stronger for zooplankton, with higher slopes and shorter halving distances, than for phytoplankton and bacteria. These results provide evidence that distance decay of similarity is related to study scale, environment, and organism characteristics. Planktonic communities may be controlled by both dispersal‐driven assembly and local ecological determinism, with the balance between these two forces depending on study scale.