Metals and radionuclides in water systems can be easily adsorbed on suspended matter and, finally, they could eventually accumulate in the aquatic environment. The assessment of the health of a water body needs also sampling of the suspended matter fraction. In this paper sampling systems to characterise contaminants associated with the suspended matter fraction are described, with a particular attention to the collection and preservation of samples. Sampling must be representative, to obtain reliable conclusions. In this context it is stressed the importance of the evaluation of the sampling uncertainty, which contributes to a large extent to the total uncertainty.