In this paper systematic studies were carried out by means of light scattering, photon correlation spectroscopy, transmission electron microscopy and bacterial analysis to investigate the evolution of colloidal samples during storage, in various conditions. The significant influence of temperature during short-term sedimentation fractionation has been shown. The time scales of coagulation of colloids and bacteria proliferation are reported as well as the significant influence of stirring in both cases. The stability of various size fractions of water samples with respect to bacterial growth has also been studied. General recommendations for performing analysis of aquatic colloids are proposed.