As the ecological and environmental consequences of microorganisms stem from the collective action of many individuals, it is paramount also to understand the physiology of microorganisms at the single-cell level. Video microscopy and microfluidics are uniquely suited to do so. We are pursuing this line of research by studying both phytoplankton and bacteria. In phytoplankton, for example, we have recently developed a system that allows us to track single cells through multiple rounds of replication. In bacteria, we utilise a quantitative phase-imaging system that measures the mass of individual cells. These efforts are yielding better insights into microbial growth dynamics. Additionally, millifluidic experiments allow us to study the transcriptomics and proteomics of bacterial populations exposed to diverse nutritional environments, from poor to rich and from steady to fluctuating.