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A swimming microorganism stirs the surrounding fluid, creating a flow field that governs not only its locomotion and nutrient uptake, but also its interactions with other microorganisms and the environment. Despite its fundamental importance, capturing this flow field and unraveling its biological implications remains a challenge. Here, we report direct, time-resolved measurements of the three-dimensional (3D) flow field generated by a single, free-swimming microalga, , a model organism for microbial locomotion and flagellar dynamics. Supported by hydrodynamic modeling and simulations, our measurements resolve how established two-dimensional (2D) flow features such as in-plane vortices and the stagnation point emerge from and shape the full algal flow in 3D. Moreover, we reveal unexpected low-Reynolds-number flow phenomena including micron-sized vortex rings and periodically recurring translating vortices and uncover topological changes in the underlying flow structure associated with the puller-to-pusher transition of an alga. Biologically, access to the 3D flow field enables rigorous quantification of the alga’s energy expenditure, as well as its swimming and feeding efficiency, improving the precision of these physiological metrics. Taken together, our study demonstrates rich vortex dynamics in inertialess flows and shows their influence on microbial motility. The work also introduces an experimental method for mapping the fluid environment sculpted by beating flagella.