Lakeshore deterioration is a major threat to the ecological integrity of lakes worldwide. In this study, the relationship between littoral benthic invertebrates and the Lakeshore Modification Index (LMI) was examined. The influence of the taxonomic resolution on littoral benthic invertebrate community response to LMI was assessed using the results of the canonical correspondence analysis and the relationship between the taxa richness, Shannon–Wiener diversity index and the LMI. Benthic invertebrates were sampled in summer between 2006 and 2011 in two natural and two artificial Alpine lakes using a littoral microhabitat type sampling scheme. Ordination analyses show a similar explanation power when the lowest available taxonomic level was used in comparison with the family level. Taxa richness and the Shannon–Wiener diversity index indicate that lakeshore modifications impair littoral biological conditions with a loss of richness and diversity independently of lake type and used taxonomic level. For 64 families, a lakeshore modification indicative value between one and nine were set on the basis of distribution among five lakeshore modification classes. A Littoral Fauna Index (LFI) was then derived by summation of the lakeshore modification indicative values recorded at each site. A validation dataset from natural and artificial lakes confirmed the good relationships between LMI and LFI but revealed some differences in the relationships. The results show that the impacts of lakeshore modifications can be assessed using littoral benthic invertebrate assemblages with a family-level-based LFI, which makes this method cost effective and appropriate for routine monitoring. Copyright © 2013 John Wiley & Sons, Ltd.