In the EU Water Framework Directive, lakes are classified into different types primarily on the basis of morphological and chemical characteristics. Lake type definition is not trivial because the different lake types may require different nutrient loading reduction targets to achieve the goal of at least "good" ecological status. Using data from 770 Danish lakes, we illustrate some of the problems associated with classification. In Denmark, 16 potentially different lake types are defined using an alkalinity boundary of 0.2 meq/L, a colour boundary of 60 mg/L Pt, a salinity boundary of 0.5 parts per thousand, and a water mean depth boundary of 3 m. However, all classification variables showed considerable seasonal and interannual variation. Most lakes with a mean depth <3 m were polymictic, but stratification depended on lake size, complicating simple classification according to depth. Conditional inference tree analyses defined relatively clearly delineated groups of macrophytes, phytoplankton, and fish based on species presence, thereby confirming the relevance of using lake type classification. Alkalinity and salinity were the 2 most important factors and defined alkalinity split points at 0.07 and 0.76 meq/L and salinity split points between 0.5 parts per thousand and 4 parts per thousand. However, with a few exceptions, the individual taxa occurred over a broad range of lake characteristics. Lake classification may be necessary for management reasons, but the absence of well-defined boundaries among lake types and a large natural variability in morphological and chemical characteristics urge cautious decisions when defining targets for external nutrient loading reduction for the various lake categories.