ABSTRACT1. Lake Habitat Survey (LHS) provides a standard method for characterizing the physical habitat of lakes and reservoirs, but has not been tested for its relevance to the composition and abundance of macroinvertebrates. This study investigated the relationship between the metrics used in LHS and components of macroinvertebrate communities found in the littoral zone of a shallow calcareous lake in the west of Ireland.2. A scoring system, the Habitat Quality Assessment (HabQA), developed from the Lake Habitat Quality Assessment (LHQA) of the LHS, was used to assess the relationship between habitat quality based on physical structure within 10 LHS 'habplots' and metrics of the macroinvertebrate community.3. Macroinvertebrate taxon richness, both of adults found in the riparian zone and larvae found in the littoral zone, correlated positively with the HabQA score. Macrophytes within the littoral zone, and complexity of riparian vegetation within the riparian zone, were particularly important in driving the HabQA score. While overall abundance of macroinvertebrates did not vary with HabQA score, that of particular genera did.4. The HabQA score was a useful surrogate of taxon richness for adult and larval aquatic macroinvertebrates, suggesting that, in general, LHS provides a useful conservation assessment tool relevant for macroinvertebrates. However, in some circumstances, such as wave-washed stony substrates devoid of macrophytes, the HabQA score may not capture the quality of a site for macroinvertebrates, and the importance of natural but low diversity sites should not be neglected in conservation assessment of lakes. Similarly, while the LHS method notes the presence of alien species, further work on how these could be incorporated into the method would be useful.5. Reliance on a single, or overall combined, metric score across quality elements, whether based on biotic or structural assessment, has some potential limitations. It is clear that for conservation management a holistic assessment of naturalness, representativeness and species rarity needs to be made in conjunction with scoring systems.