The characterization of lake hydromorphology is crucial to understand the dynamics of biodiversity. In Europe, it is also a regulatory requirement of the Water Framework Directive. However, according to the literature, few methods include this characterization. The aim of this study is to review the state of the art of the methods currently used or under development in European countries to assess lake hydromorphological status for the implementation of the WFD. Our analysis is based on responses to a questionnaire distributed to national experts on hydromorphology of the 28 countries implementing the WFD. Our results highlighted significant progress in the assessment of hydromorphological features and processes. Water level regime, through the range of water flow or existing water management, and structure of the shore zone through macrophytes and substrate characteristics or measurement of lateral connectivity, are the most frequently assessed features. Stratification, surface/groundwater connection and planform pattern are the lake features most frequently omitted from the methods. However, in most of the countries, the development of methods was still in progress to meet the WFD requirement. Definition of reference condition is a central component of all WFD compliant assessment tools but this is a challenge particularly in the assessment of hydromorphological alteration of reservoirs. Similarly, demonstrating strong links between hydromorphological indicators and biological quality elements remains a challenge with many knowledge gaps still evident. These results highlight the need for rapid collection of new environmental data and the need for conceptual and applied research to make methodological progress in assessing lake hydromorphology and ensuring habitat quality.