The literature proposes that bacterial abundance (BA) and heterotrophic nanoflagellates abundance (HNFA) are positively related across different aquatic systems, suggesting a strong resource control of HNFA and predatory control of BA. To test this proposed pattern, we collected published and unpublished data and analyzed trends across lakes, rivers, marine, and benthic samples. BA varied between 105 and 1011 cells ml−1, while HNFA ranged from 102 to 106 cells ml−1. The relationship was stronger in systems with low bacterial abundances and weaker in the most bacteria‐rich systems. When data were averaged per study or per system we detected a trend with trophy, with highest HNFA in benthic systems followed by lakes and coastal areas of the sea, and lowest abundances in rivers and the open ocean. This relationship was improved in lakes, where cladoceran abundance was negatively related to HNFA. The effect of cladocerans was stronger in lakes where Daphnia spp. dominated. The weak pattern observed between BA and HNFA across systems suggests that several factors (resources, predators, environment, etc.) are acting differently on BA and HNFA. Changes in population abundances of bacteria and heterotrophic nanoflagellates are mainly determined by nutrient supply and grazing, and also by complex trophic interactions with numerous feedbacks. Empirical relationships between BA and HNFA across systems can only partially explain these changes in terms of predator‐prey dependence.