The puzzling persistence of nanobubbles breaks Laplace's law for bubbles, which is of great interest for promising applications in surface processing, H2 and CO2 storage, water treatment, and drug delivery. So far, nanobubbles have mostly been reported on hydrophobic planar substrates with atomic flatness. It remains a challenge to quantify nanobubbles on rough and irregular surfaces because of the lack of a characterization technique that can detect both the nanobubble morphology and chemical composition inside individual nanobubble-like objects. Here, by using synchrotron-based scanning transmission soft X-ray microscopy (STXM) with nanometer resolution, we discern nanoscopic gas bubbles of >25 nm with direct in situ proof of O2 inside the nanobubbles at a hydrophilic particle-water interface under ambient conditions. We find a stable cloud of O2 nanobubbles at the diatomite particle-water interface hours after oxygen aeration and temperature variation. The in situ technique may be useful for many surface nanobubble-related studies such as material preparation and property manipulation, phase equilibrium, nucleation kinetics, and relationships with chemical composition within the confined nanoscale space. The oxygen nanobubble clouds may be important in modifying particle-water interfaces and offering breakthrough technologies for oxygen delivery in sediment and/or deep water environments.