Groundwater vulnerability maps are useful for environmental planning and decision-making. They are usually produced by applying vulnerability assessment methods using overlay and index techniques. On the basis of a review of the vulnerability assessment and mapping methods, new research challenges in aquifers vulnerability assessment are identified. Operations like the parameter quantification, the vulnerability index computing, and the final classification, are affected by an empirical character which of course affects also the final product: the vulnerability map. In consequence, the validity of the resulted vulnerability maps must be evaluated in function of the objectives of the survey and in function of the specific characteristics of each studied zone. Analysing their uncertainty can represent the base for their validation. Uncertainty can be investigated through sensitivity analysis or through comparisons between vulnerability maps created using different methods. Both these strategies are developed in this study and illustrated from applications on practical case studies of vulnerability mapping. Applying the EPIK parametric method, a vulnerability assessment has been made for a small karstic groundwater system in southern Belgium. The aquifer consists in a karstified limestone of Devonian age. A map of intrinsic vulnerability of the aquifer shows three vulnerability areas. A parameter-balance study and a sensitivity analysis were performed to evaluate the influence of single parameters on aquifer vulnerability assessment using the EPIK method. This approach provides a methodology for the evaluation of vulnerability mapping and for more reliable interpretation of vulnerability indices for karst groundwater resources. Five different methods for assessing the intrinsic vulnerability were tested on a case study for comparison of their results. The test area consists in a slightly karsified basin located in the Condroz region (Belgium). The basin covers about 65 km² and the karstic aquifer provides a daily water supply of about 28000 m³ in drainage galleries. Several campaigns of measurements consisting in morpho-structural observations, shallow geophysics, pumping and tracer tests have provided useful data. The tested methods were: EPIK (Doerfliger and Zwahlen, 1997), DRASTIC (Aller et al., 1987), German methods (von Hoyer & Söfner, 1998), GOD (Foster, 1987), and ISIS (Civita and De Regibus, 1995). DRASTIC and GOD represent classic approaches in vulnerability assessment. ISIS is a development based on DRASTIC, SINTACS (Civita, 1994), and GOD methods, where more importance is given to the recharge. EPIK was developed specifically for karstic geological contexts and the German methods was developed in Germany for a broad range of geological contexts. Compared results are shown and commented. It seems that despite the fact that the EPIK method can better outline the karstic features about 92% of the studied area is assessed by this technique as low vulnerable. In contrast, the other four methods are considering extended zones of high or moderate vulnerability. From the analysis, it seems also that reducing the number of considered parameters is not ideal when adaptation to various geological contexts is needed. Reliability and validity of groundwater analysis strongly depend on the availability of large volumes of high quality data. Putting all data in a coherent and logical structure supported by a computing environment helps ensure a validity and availability, and provides a powerful tool for hydrogeological studies. A hydrogeological GIS database that offers facilities for groundwater vulnerability analysis and hydrogeological modelling has been designed in Belgium, for the Walloon Region. Data from five river basins, chosen for their contrasted applications that have been developed allow now further advances. However the basic concept of the database is represented by the commonly accepted Georelational model developed in the 1970s, the database concept presents a distinctive character. There is a growing interest in the potential for integrating GIS technology and groundwater simulation models. Between the mentioned spatial database schema and the groundwater numerical model interface GMS (Groundwater Modelling System) a loose-coupling tool was created. Following time and spatial queries, the hydrogeological data stored in the database can be easily used within different groundwater numerical models. This development can represent also a solid base for the physical processes integration within the quantification of the vulnerability methods parameters. The fundamental aim of this work was to help improving the aquifers protection strategy using vulnerability mapping and GIS. The results are offering the theoretical and practical basis for developing a strategy for protecting the groundwater resources.