This paper presents selected results of research connected with the development of a (3D) geostatistical hydrogeochemical model of the Kłodzko Drainage Basin, dedicated to the spatial variation in the different quality parameters of underground water in the water intake area (SW part of Poland). The research covers the period 2011–2012. Spatial analyses of the variation in various quality parameters, i.e., contents of: iron, manganese, ammonium ion, nitrate ion, phosphate ion, total organic carbon, pH redox potential and temperature, were carried out on the basis of the chemical determinations of the quality parameters of underground water samples taken from the wells in the water intake area. Spatial variation in the parameters was analyzed on the basis of data obtained (November 2011) from tests of water taken from 14 existing wells with a depth ranging from 9.5 to 38.0 m b.g.l. The latest data (January 2012) were obtained (gained) from 3 new piezometers, made in other locations in the relevant area. A depth of these piezometers amounts to 9–10 m. Data derived from 14 wells (2011) and 14 wells + 3 piezometers (2012) were subjected to spatial analyses using geostatistical methods. The evaluation of basic statistics of the quality parameters, including their histograms of distributions, scatter diagrams and correlation coefficient values r were presented. The directional semivariogram function γ(h) and the ordinary (block) kriging procedure were used to build the 3D geostatistical model. The geostatistical parameters of the theoretical models of directional semivariograms of the water quality parameters under study, calculated along the wells depth (taking into account the terrain elevation), were used in the ordinary (block) kriging estimation. The obtained results of estimation, i.e., block diagrams allowed us to determine the levels of increased values of estimated averages Z* of underground water quality parameters.