The project “National Groundwater Flow System Analysis” in The Netherlands was initiated in 1991 and will last until 1995. Financed by three Dutch Ministries, the project aims at the mapping of the regional groundwater flow systems to support policy makers at national levels and water/nature resources management. Much emphasis is put on biotic aspects such as the relation between groundwater and patterns in vegetation. The results are used in a detailed flow system analysis of the eco-hydrological valuable drainage basin of the brooks Beerze and Reusel in the southern parts of the country. In this study vegetation patterns and hydrological situations were analyzed in present and in historical settings to unravel the changes in the last decades leading to severe deterioration of habitats and wetlands. Historical data on flora from the beginning of this century on the basis of km-grid cells show a strong relation with the historical exfiltration areas where deep alkaline groundwaters rich in calcium-carbonate emerged. Agriculture and man-made changes to the natural drainage systems have led to diminishing nature values. Combining a sound understanding of the groundwater flow systems and the changes in the last decades produced a number of practical and viable measures to restore historical wetland settings and to preserve existing ones.