Morphotypes for 67 lakes in the German lowlands were derived, based on maximum depth and mixis type. A threshold of 11 m maximum depth was identified to be the best level to discriminate shallow from deep lake morphotypes. The fish communities in these two morphotypes were significantly different. Indicator species analyses based on fish biomasses found vendace Coregonus albula in deep lakes and ruffe Gymnocephalus cernuus, bream Abramis brama, white bream Abramis bjoerkna, roach Rutilus rutilus, pikeperch Sander lucioperca and small perch Perca fluviatilis in shallow lakes to be the most representative species of their communities. Lake productivity was closely related to biomass and in part abundance of the type-indicator species, with vendace declining with increasing chlorophyll a concentration in the deep lakes, whereas biomass of pikeperch, bream, white bream and ruffe increased and biomass of small perch decreased with increasing chlorophyll a. These results indicate that assessment of ecological integrity of lakes by their fish fauna is generally possible, if lakes are initially separated according to a depth-related morphotype before the assessment, and if eutrophication is considered to be the main anthropogenic degradation.