Understanding the mechanisms that govern biological diversity in various environments is one of the greatest challenges for the scientific community of today. Compared to terrestrial and benthic habitats, mechanisms regulating species diversity in planktonic ecosystems have been dealt with relatively little. This is mainly due to the scarcity of the experimental evidence from field studies where the multitude of spatiotemporal scales have been covered with sufficient resolution. This paper discusses the pecularities of the aquatic system as a growth environment for phyto-plankton in comparison to terrestrial/connected systems. Examples of the regulation of species diversity in the Baltic Sea are presented.