Despite great efforts in point source reductions due to improved wastewater treatment since 1990, more than 70% of the lakes in Germany have not yet achieved the “good ecological status” according to the European Water Framework Directive (WFD). To elicit lake type-specific causes of this failure, we firstly analyzed the ecological status of 183 lakes in NE Germany (Federal State of Brandenburg), as reported to the European Commission in 2015. Secondly, long-term data of two typical lakes (a very shallow polymictic lake with a large and a deep stratified lake with a small catchment area in relation to lake volume) and nutrient load from the common catchment were investigated. About 64%–83% of stratified and even 96% of polymictic shallow lakes in Brandenburg currently fail the WFD aims. Excessive nutrient emissions from agriculture were identified as the main cause of this failure. While stratified deep lakes with small catchments have the best chances of recovery, the deficits in catchment management are amplified downstream in lake chains, so that especially shallow lakes in a large catchment are unlikely to reach good ecological conditions. If the objectives of the WFD are not questioned, agricultural practices and approaches in land use have to be fundamentally improved.
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