Eutrophication leads to epiphyte blooms on seagrass leafs, which strongly affect plant health, yet the actual mechanisms of such epiphyte‐induced plant stress remain poorly understood. We used magnetic optical sensor nanoparticles in combination with luminescence lifetime imaging to map the O2 concentration and dynamics in the heterogeneous seagrass phyllosphere under changing light conditions. By incorporating magnetite into the sensor nanoparticles, it was possible to image the spatial O2 distribution over the seagrass leaf segments under flow in the presence of a strong magnetic field. Local microniches with low leaf surface O2 concentrations were found under thick epiphytic biofilms, often leading to anoxic microhabitats in darkness. High irradiance led to O2 supersaturation across most of the seagrass phyllosphere, whereas leaf microenvironments with reduced O2 conditions were found under epiphytic biofilms at low irradiance, likely driven by self‐shading. Horizontal microprofiles extracted from the O2 images revealed pronounced heterogeneities in the local O2 concentration over the base of the epiphytic biofilm, with up to 52% reduction in O2 concentrations in areas with relatively thick (>2mm) as compared to thin (≤1mm) epiphyte layers in darkness. We also present evidence of enhanced relative internal O2 transport within leaves with epiphyte overgrowth as compared to bare seagrass leaves in light, due to limited mass transfer across thick outward diffusion pathways. However, the local O2 availability was still markedly reduced in the epiphyte‐covered leaves. The leaf phyllosphere is thus characterised by a complex micro‐landscape of O2 availability, which strongly affects microbial processes occurring within the epiphytic biofilm, that may have implications for seagrass health, as anoxic microhabitats have been shown to promote microbiological production of reduced toxic compounds such as nitric oxide.