Microorganisms form the base of marine food webs and drive global biogeochemical cycles, yet their responses to unsteady and chaotic flows remain poorly understood despite the prevalence of such environments, as fluid motion exerts physical forces while shaping chemical landscapes critical for sensing, foraging, and reproduction. Here, we present a Lagrangian framework—built upon Lagrangian coherent structures (LCSs)—to investigate the transport and dynamics of swimming microorganisms in chaotic flows, offering a geometrically precise alternative to conventional Eulerian approaches. We examine interactions with hyperbolic LCSs, where microbial alignment and accumulation near these attracting or repelling material surfaces suppress large-scale dispersal while enhancing small-scale mixing, with implications for plankton patchiness. We then explore interactions with elliptic LCSs—rotation-dominated vortex-like structures—and find that microorganisms tend to escape and deplete within these features, reinforcing transport barriers for passive scalars such as temperature and salinity. These findings enable quantitative predictions of microbial transport in chaotic flows and provide insights into harmful algal bloom spread and oil-spill mitigation. More broadly, this work demonstrates the power of Lagrangian diagnostics in bridging organism-scale behavior with mesoscale ocean dynamics, illustrating how cross-scale physical–biological coupling can be characterized through flow structures. By providing a mechanistic link between small-scale biological responses and submesoscale to mesoscale physical variability, this study highlights the potential of LCS-based approaches—complementary to high-resolution observations and numerical models—for advancing integrated physical–biogeochemical–ecological understanding.