A novel approach to study nanomechanical properties such as deformation, adhesion or Young's modulus is presented for freshwater diatoms having sizes ranging from tens to hundreds of micrometers. Changes occurring in the environment, such as water acidity or temperature variations, have an impact on the diatoms population, as they can cause the death of certain species favoring simultaneously the growth of another. The nanomechanical properties were measured by means of atomic force microscopy (AFM) in a unique PeakForce tapping (PFT) mode. The observed changes of the Young's modulus measured in the frustule of Cyclotella meneghini diatom were in the range of 7–25 GPa, clearly confirming that, in this part of the diatom, degeneration occurs. The use of the PFT mode in the AFM allowed also for measuring the surface of diatoms exhibiting a very developed topography. This is a new methodology for quantitative measurements of nanomechanical properties allowing to monitor environmental changes. Copyright © 2014 John Wiley & Sons, Ltd.