1. Hydromorphology provides a physical framework for aquatic biocenoses. Its condition directly affects the quality of habitats available for fauna and flora, and its assessment is therefore useful for biodiversity and water quality conservation, as well as for restoration programmes required by European and national directives. 2. In this study, a site‐specific index of Lake HYdroMOrphology, LHYMO, was developed to provide a quantitative assessment of the hydromorphological status of natural and non‐natural lakes that is consistent with European Committee for Standardization (CEN) standards and that can be used for different purposes, including the implementation of the Water Framework Directive (WFD) and of the Habitats Directive. 3. This new LHYMO index includes nine metrics related to the morphological WFD quality elements (QEs) and six metrics related to the hydrological WFD QEs, all of which are considered to support biological elements. The reference conditions were defined for each metric using an original approach: the degree of alteration is measured in relation to the natural characteristics of each lake, relative to a state that ‘would be expected in the absence of disturbances’. 4. Besides its use for regulatory purposes, this index is also a suitable tool for monitoring the efficacy of hydromorphological restoration projects or to help target effective conservation measures on lakes. 5. Application of this index to 72 French lakes provides the first quantitative and homogeneous assessment of the hydromorphological quality of lakes over a whole territory and gives the first overview of the hydromorphological status of lakes in France, with classification into five classes ranging from ‘high’ to ‘bad’. 6. LHYMO is already operational for large French lakes as it relies mostly on reference datasets available at a national scale, and it may also be used in a wider scope through gathering or completing data from other sources.