Hydrogeological parameters of an aquifer change by diagenetic processes due to water-rock interaction. The clay fraction which exists in the matrix of sedimentary aquifers even in minute quantity has great importance in these processes. The resulting change may influence the flow regime. One of the zones most affected by diagenesis is where two chemically different types of water meet. Numerous coastal aquifers, including the one in Israel, contain chemically different types of water, and, consequently, many interfaces. The degree of alteration of hydrogeological parameters was studied in the laboratory under the extreme conditions of a seawater/fresh-water interface; where a large decrease of hydraulic conductivity was observed. One can use the findings of this laboratory study in building a model of prediction for the influence of water-rock interaction on the flow in other interfaces of an aquifer.