Atomic force microscopy (AFM) is used to investigate the topography and material properties of the mucilage layer of live cells of three benthic diatoms, the marine species Crasepdostauros australis E. J. Cox and Nitzschia navis-varingica Lundholm et Moestrup and the freshwater species Pinnularia viridis (Nitzsch) Ehrenberg. Contrary to previous studies, we show that this surface mucilage layer displays unique nanostructural features. In C. australis, tapping mode images revealed a soft mucilage layer encasing the silica cell wall, consisting of a smooth flat surface that was interrupted by regions with groove-like indentations, whereas force measurements revealed the adhesive binding of polymer chains. The elastic responses of these polymer chains, as they were stretched during force measurements, were successfully fitted to the worm-like chain model, indicating the stretching of mostly single macromolecules from which quantitative information was extracted. In P. viridis, tapping mode images of cells revealed a mucilage layer that had the appearance of densely packed spheres, whereas force measurements exhibited no adhesion. In N. navis-varingica, tapping mode images of the outer surface of this cell in the girdle region revealed the absence of a mucilage layer, in contrast to the other two species. In addition to these topographic and adhesion studies, the first quantitative measurement of the elastic properties of microalgal extracellular polymeric substance is presented and reveals significant spatial variation in the C. australis and P. viridis mucilage layers. This study highlights the capacity of AFM in elucidating the topography and mechanical properties of hydrated microalgal extracellular polymeric substance on a nanoscale.