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Implementation of the EU Water Framework Directive (WFD) has drawn much attention to hydromorphological alterations of surface waters. The Lake Habitat Survey (LHS) protocol provides a method for characterising and assessing the physical habitats of lakes and reservoirs. Two metrics were developed based on this method: the Lake Habitat Modification Score (LHMS) and the Lake Habitat Quality Assessment (LHQA), as measures of lake modification and habitat value, respectively. However, the use of these metrics to predict measures of ecological quality remains largely untested. Thus, we assessed the relationships between LHS metrics and the littoral macroinvertebrate community in 42 lakes across Europe. A significant relationship was found between littoral macrophyte descriptors and riparian natural land cover variables of the LHQA score and macroinvertebrate community composition in 2 out of 4 European regions. No relationship was found between macroinvertebrate community composition and the LHMS. Some significant correlations were found between selected macroinvertebrate metrics and the LHS scores, but this pattern was not consistent across regions, and no relationship was found with the overall LHMS or LHQA scores. This demonstrates that the LHS metrics do not consistently predict the quality of littoral macroinvertebrate communities across Europe, and a region specific approach may be necessary. However, we could demonstrate a relationship between the site specific LHS variables and the macroinvertebrate community at the site level, and in some cases at the regional level. Therefore, although the LHS metrics do not appear to be a useful for relating habitat quality and pressure to littoral macroinvertebrate communities, selected LHS variables may exhibit stronger relationships with the biota.