1. In the absence of a standard procedure for characterizing the physical habitat of lakes in Europe, this paper describes the development of a multi-purpose Lake Habitat Survey (LHS). The technique has been designed to meet the hydromorphological assessment needs of the Water Framework Directive (WFD), as well as to assist in monitoring the condition of designated sites in the UK and for wider application in environmental impact assessments and restoration programmes. 2. LHS involves detailed recording of shoreline features at a number of plots (Hab-Plots), complemented by a meso-scale survey of the entire lake, including shoreline characteristics and pressures, and modifications to the hydrological regime. A temperature and dissolved oxygen profile is also compiled at the deepest point of the lake (Index Site). Existing databases are exploited where possible, and remote sensing data (e.g. aerial photographs) are used to assist field-based observations. 3. Initial field trials demonstrated that the consistency of the method, whether conducted by boat or on foot, was high. More than 250 surveys were carried out across the UK in 2004 through collaboration with the statutory environment and conservation agencies. 4. Two levels of complexity were tested — a full version requiring 10 Hab-Plots and an abridged version, LHScore, involving four plots and omitting the Index Site. While 8–10 plots were required to capture the full diversity of features at complex sites, LHScore data were sufficient to generate metrics for classification purposes. 5. A Lake Habitat Modification Score (LHMS) may be calculated from LHS data. This synthesizes a wide array of hydromorphological and human pressures and has direct applications for assessment of ecological status under the WFD. Preliminary analysis illustrates a spectrum of hydromorphological alteration of 82 lakes in the UK. 6. Further considerations are discussed, including the prospect that the LHS protocol might form the basis of a European standard developed through CEN (Comite Europeen de Normalisation). Copyright © 2006 John Wiley & Sons, Ltd.