The Low Temperature Method (LTM) for sample stabilization in environmental scanning electron microscopy (ESEM) is a promising tool for observing diatom assemblages in vivo. Use of ESEM, in comparison to conventional scanning electron microscopy, enables fresh material to be studied without any chemical pretreatment or conductive coating. The newly developed LTM, introduced in this paper, offers higher resolution and better resistance of wet samples to radiation damage. We used natural epiphytic algal assemblages to image the 3D structure of: (i) biofilm/periphyton and its physical complexity, (ii) diatoms with their extracellular mucilaginous secretions attaching cells to the substratum, (iii) diatom colony formation, and (iv) intact diatom cells, rather than the separated empty valves observed under conventional scanning electron microscopy. This study demonstrates the potential of the LTM for ESEM in diatom biology and ecology compared to other imaging methods.