Despite differences in the species compositions and absolute abundances of planktonic microorganisms in fresh-and saltwater, there are broad similarities in microbial food webs across systems. Relative abundances of bacteria and nanoplanktonic protozoa (HNAN, primarily heterotrophic flagellates) are similar in marine and freshwater environments, which suggests analogous trophic relationships. Ranges of microbe abundances in marine and fresh waters overlap, and seasonal changes in abundances within an ecosystem are often as great as differences in abundances between freshwater and marine systems of similar productivities. Densities of bacteria and heterotrophic nanoplankton, therefore, are strongly related to the degree of eutrophication, and not salt per se. Data from the literature is compiled to demonstrate a remarkably consistent numerical relationship (ca 1000 bacteria: l HNAN) between bacterioplankton and HNAN from the euphotic zones of a variety of marine and freshwater systems. Based on the results of a simple food web model involving bacterial growth, bacterial removal by HNAN, predation on HNAN, and the observed relationships between bacterial and HNAN abundances in natural ecosystems, it is possible to demonstrate that bottom-up control (food supply) is more important in regulating bacteiial abundances in oligotrophic environments while top-down control (predation) is more important in eutrophic environments.