Bridging the gap between policy aspirations and the ability of regulators to deliver robust evidence-based tools within affordable and realistic time-scales presents major challenges to the science community. Lake-MImAS (Morphological Impact Assessment System) is a hydromorphological classification and decision-support tool adaptable to any setting, developed in response to the EC Water Framework Directive (WFD) requirement to classify all surface waters in the European Union and achieve at least good ecological status by 2015. Lake-MImAS provides a transparent and consistent risk-assessment framework to assess the impact of hydromorphological pressures on ecologically relevant lake features and associated processes. Underpinned by expert-judgement, the tool quantifies lost 'system capacity' (%) relative to pristine, or un-impacted condition and does so on a type-specific basis. Morphological condition limits (MCLs) separate 'lost capacity' into five condition classes ranging from near natural to severely altered. Near natural (<5% capacity loss) corresponds directly with high ecological status of the WFD and provides the basis to define reference conditions. The calibrated tool was tested against independent judgement made by expert practitioners from UK environment and conservation agencies. The same condition class was assigned in 84% of Scottish lochs (. n=. 40), in 58% of lakes in England and Wales (. n=. 28) and in 57% of loughs in Northern Ireland (. n=. 27). The overall agreement was 68% and 98% of all comparisons lay within one condition class. In most cases where different classes were assigned the explanation lay in local experts underestimating the extent of water level regulation. Whilst further work is required to strengthen the evidence base linking hydromorphological alteration and ecological response, Lake-MImAS provides the foundation for a pragmatic risk-assessment scheme to support WFD classification and related regulatory activity. The modular nature of the tool means it adaptive to new locations, lake type and pressure combinations and it has wider applications including physical condition monitoring for conservation sites, impact assessment arising from new developments and supporting remediation programmes. © 2011 Elsevier Ltd.