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Microorganisms are critically important for ecological processes in aquatic environments. Bacteria and viruses are key components of the microbial loop and are central for biogeo‐ chemical cycles in aquatic ecosystems. Our group has been using transmission electron microscopy (TEM) to study aquatic microorganisms in both natural tropical ecosystems and cultures. In this review, we highlight structural aspects of freshwater bacteria, based on TEM findings that have provided insights into the functional capabilities of these cells in aquatic tropical ecosystems. First, we focus on TEM applied to the study of the ultra‐ structural diversity and morphological alterations of bacteria in response to environmen‐ tal stress. Second, we address the relationship between viruses and bacteria in freshwater ecosystems. Third, we demonstrate by TEM that outer membrane vesicles (OMVs), struc‐ tures associated with cell secretion and cell communication, are released by aquatic bacte‐ ria into natural ecosystems and cultures. Thus, TEM has proven to be a powerful technique to study aquatic microorganisms, contributing to the understanding of ecologi‐ cal processes, including regulation of bacterial populations, during different environmen‐ tal conditions.

TEM as an Important Tool to Study Aquatic Microorganisms and their Relationships with Ecological Processes