Lakes provide many ecosystem services such as drinking-water supply and recreation. Restoration measures are needed in case of severe impairments by human activities. Eutrophication is the major cause of lake alteration. It is due to intensive agriculture or input of sewage and is characterized by high nutrient concentrations. The main consequences of eutrophication are high primary production, low water transparency and hypolimnic anoxia. Effective restoration requires the reduction of nutrient input to the lakes and precise objectives in terms of quantitative water quality targets have to be set. Physico-chemical standards are often derived statistically from the distribution of parameters among sites. However, such standards lack ecological relevance because they are not linked to the response of biological elements. Ecological community thresholds are zones in the gradients of environmental parameters where variations in species abundance are enhanced relative to the rest of the gradient. They may provide more meaningful restoration targets. In this study, the method of gradient forest was used to detect community thresholds from a database of about 200 hundreds French lakes and reservoirs. The analysis was performed on phytoplankton, macrophytes and fish data, separately. Community thresholds derived from the three biological groups are compared with a focus on two parameters: total phosphorus concentration and water transparency. Some thresholds are similar among groups revealing possible important ecological thresholds, whereas others are specific of a particular group. A framework is proposed to use these thresholds in combination with estimated reference conditions to determine site-specific water quality restoration targets.