Mathematical expressions have been widely used to describe and simulate complex physical processes encountered in nature. For the majority of simple physical problems an analytical solution can be obtained using well-known conventional analytical methodologies whereas numerical methodologies are used to obtain solution in complex linear or non-linear design problems. In this paper, a comparison of two different computational methods, focusing on Finite-element and Finite-difference methods, is presented for the solution of complex environmental design problems. Also, in order to analyse and evaluate the most used geostatistical methodologies for spatial data interpretation the complex coastal aquifer of Hersonissos in Crete was chosen and a groundwater simulation model was developed.