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This document gives guidance on procedures for the pro-rata multi-habitat sampling of benthic macroinvertebrates in rivers and streams. The term “pro-rata” reflects the intention to sample all the main riverine habitats present at a monitoring site according to the proportion of the site that it covers. It is an objective way to divide sampling effort among the different habitats. This guidance is applicable to all flowing waters, both artificial, modified and natural. This design enables comparable samples to be collected from any type of river, regardless of the habitats present. The pro-rata multi-habitat sampling is an overall approach rather than a specific method. This document is designed to: - support environmental and conservation agencies to meet the monitoring requirements of the WFD (Article 8, Annex II, and Annex V); - generate data sets appropriate for monitoring and reporting of sites designated under the Habitats Directive and the Birds Directive ensure that samples for comparing the overall composition of invertebrates from different stream types are comparable; - ensure samples for environmental quality assessments across different stream types are comparable even when sampled by different people; and - support river management and restoration initiatives. The pro-rata multi-habitat sample (MHS) provides: - a consistent way of sampling sites that is not dependent on the presence of particular types of habitat; and - guidance on a user-friendly strategy for collecting biological data depending on the distribution of substrate type. It is also ideal for: - understanding the distribution of biological community types across different physical river types; and - quality assessments based on deviation from reference, as adopted in the European Water Framework Directive.