Several ecological and hydromorphological assessment methods have been developed in different countries during the last years, with notable differences in terms of aims, scales, and approaches. In many cases, strengths and limitations of the different types of methods are not yet sufficiently known, although they are widely used in some European countries. The objective of this report is to provide an extensive overview of the eco-hydromorphological assessment methods that are available for the implementation of the WFD and to identify strengths, limitations, gaps, possible integration of different approaches, and needs for future progress.  The main emphasis is on ‘hydromorphological assessment methods’, i.e., methods and procedures developed and used to characterize hydromorphological conditions and classify the status of streams and rivers, including a review of indicators and parameters used within this context.

For this review, five broad categories of hydromorphological assessment methods have been distinguished: (1) Physical habitat assessment; (2) Riparian habitat assessment; (3) Morphological assessment; (4) Hydrological regime alteration assessment; (5) Longitudinal fish continuity assessment. The first stage was to review the general characteristics of a total of 139 methods (European and non-European). For each category, the main information concerning each method has been summarized, allowing for a comparative analysis of the methods. The second stage focused on a selection of European methods (in total 21), i.e., those methods that have been formally approved or that are commonly used (although without formal approval) by European countries for the WFD implementation. For each method, the scope, characteristics, recorded features and indicators, processes and strengths have been summarized. Ecological assessment methods in use for determining the ecological status of European rivers were also reviewed. The review covers the methods that are being used by the EU countries to monitor ecological status. A total of 91 methods were considered, covering fish fauna, macrophytes, benthic diatoms, and benthic invertebrates from 27 European countries.

A series of strengths and limitations have been identified. The main gap is the insufficient consideration of physical processes in the assessment of hydromorphological conditions. With few exceptions, hydromorphological analysis adopted in most EU countries is limited to a physical habitat assessment, which is only one component of an overall hydromorphological evaluation. This is an important limitation because a characterization of physical habitats alone does not provide sufficient understanding of alterations or their causes and of pressure-responses (i.e., causes-effects), that are extremely important for the implementation of rehabilitation measures.

We recommend developing a framework for integrated hydromorphological analysis, where the morphological and hydrological components are key parts of the evaluation along with classification of hydromorphological state and quality, while physical habitat and longitudinal fish continuity should represent additional components that are useful for a complete characterization of hydromorphological conditions.

The review of existing ecological methods has also identified some additional limitations, particularly in their ability to respond to hydromorphological pressures. Methods using fish fauna, macrophytes, and benthic invertebrates are not pressure-specific; they will detect effects of multiple pressures, including hydromorphological pressures. Little information is available on the specific response of individual methods to hydromorphological pressures. Supplementary information characterizing the pressures (hydromorphological and other) is required to identify problems and to plan appropriate measures.