Particles in lake water samples originating from the Swiss lakes of Zurich and Constance were analysed, showing an exponential increase of particle number with decreasing particle size down to the detection limit (350 nm). Investigation of nanoparticles in Lake Zurich by microscopic methods showed that relatively large numbers of clay particles are present with different Al/Si composition and sizes. The small-sized clay particles (ca. 80 nm) tend to build aggregates with a size of 500–1,000 nm. In karstic spring water, the particle count and size distribution is strongly dependent on the precipitation rate. At high precipitation rates, channel flow occurs in the subsoil, leading to high particle counts among the whole size range and a larger average particle size. In membrane treatment by microfiltration and ultrafiltration this leads to membrane fouling due to pore blocking and cake formation, the latter being associated with the presence of organic compounds.