The control of the quality of shallow water at the hydrological basin of the river Keriti at Chania through chemical analyses and correlation of the physical and chemical parameters constitutes the subject of the research which is carried out under the framework of the research program of ARCHEMIDIS II. Samples of water were collected during the period 2004-2005 from 9 separate locations along the hydrological basin of the river. The parameters that were analyzed included concentrations of pH, EC, BOD, COD, TOC ΝΟ3-Ν, ΝΗ4-Ν, PΟ3-P, Cl-, as well as the micro bacterial parameters. The results were depicted on the digital elevation model and its subsequent products. Topographical maps (1:5000) of the Geographical Service of the Hellenic Army were digitized and thematic surface maps were created within the environment of Geographical Information Systems indicating the time-change of the parameters. The processing of the data through chemical analyses and mapping techniques offers a valuable tool for the valid monitoring and management of the quality parameters of water resources and for the risk assessment in cases of a pollution incidence.