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work Directive aims to achieve a ‘good’ ecological status for groundwater bodies, for groundwater-dependent terrestrial ecosystems, and for aquatic surface water bodies by the year 2015. In Denmark, this goal will most likely not be fulfilled within such a short time frame due to the current poor ecological condition of Danish lakes (Søndergaard et al. 2008). However, public concern about the protection of aquatic environments has increased, and so has interest in improving lake water quality by reducing nutrient loading. Effective and sustainable lake restoration and conservation depend on the ability to (1) point out sensitive catchment areas for the lake, (2) estimate its total water and nutrient budgets and (3) relate observed differences in seepage rates to the abundance and distribution of macrophytes in the lake and to the topography and land-use of the surrounding terrain. In seepage lakes, i.e. lakes without inlets or outlets, the influence of the surrounding terrain, regional hydrogeology and lake geometry on the overall lake water budget has been studied in some detail (Krabbenhoft et al. 1990; Anderson & Cheng 1993; Cheng & Anderson, 1994; Kratz et al. 1997; Water budget of Skærsø, a lake in south-east Jylland, Denmark: exchange between groundwater and lake water