Abstract Eutrophication impairs lake ecosystems at a global scale. In this context, as benthic microalgae are well-established warnings for a large range of stressors, particularly nutrient enrichment, the Water Framework Directive required the development of diatom-based methods to monitor lake eutrophication. Here, we present the diatom-based index we developed for French lakes, named IBDL. Data were collected in 93 lakes from 2015 to 2020. A challenge arose from the discontinuous pressure gradient of our dataset, especially the low number of nutrient-impacted lakes. To analyze the data we opted for the so-called “Threshold Indicator Taxa ANalysis” method, which makes it possible to determine a list of “alert taxa”. We obtained a multimetric index based on different pressure gradients (Kjeldahl nitrogen, suspended matter, biological oxygen demand and total phosphorous). The IBDL proved to be particularly relevant as it has a twofold interest: an excellent relationship with total phosphorus and possible application to any lake metatype. Its complementarity with macrophyte-based indices moreover justifies the use of at least two primary producer components for lake ecological status classification.