“Oligotrophic waters containing very few minerals of sandy plains” (code 3110) and “Natural dystrophic lakes and ponds” (code 3160) are two protected lake habitats under Annex I of the European Union Habitats Directive, despite this, their conservation condition is considered unfavourable in most European biogeographic regions. The available classifications rely heavily on water chemistry and phytosociology while leaving other taxa under described. This study used Coleoptera and Odonata communities as a monitoring tool to characterise and distinguish both lake habitat types. Samples were collected from 24 sites in western Ireland over two seasons (spring and summer) using standard sweep netting methods. Despite considerable overlap in assemblages, communities were shaped by lake habitat type, sampling region and season, where lake habitat 3110 hosted a higher diversity of taxa in summer dominated by dragonflies associated with larger, warmer oligotrophic waters, while lake habitat 3160 reflected higher beetle fauna in spring resembling small, turbid, stagnant waterbodies. This research highlights the potential use of aquatic invertebrates as an important monitoring tool for these lake habitats, serves to deepen the current knowledge and fill gaps in their classification, hence improving their conservation condition assessment methods for Member States when reporting under the Habitat Directive.