This paper aims to evaluate the water quality along the mainstream of the Nile in Egypt through modelling spatial distributions of water quality, using spatial statistical analysis. The study is based upon a sample frame of 78 sampling points collected in “February 2008” and located on the main waterway of the Nile and its delta (Rosetta and Damietta branches). Two water quality indices are calculated as general indicators of the overall water quality of the Nile, with special emphasis on drinking water quality. Exploratory spatial data analysis is carried out on the water quality indices, followed by plotting and modelling the experimental semi-variograms. Then, cross validation is executed in order to determine the best fitted models. Finally, surface maps are generated by performing spatial interpolation, using kriging technique. The generated surface maps of the two water quality indices show that water quality in Upper Egypt is excellent, in general, whereas water unfit for drinking is dominant in Middle and Lower Egypt. Therefore, intensive physical and chemical disinfection treatments are becoming pressing options for improving the quality of drinking water.