Many streams in the extensive Central European region have an intermittent flow regime. Conventional hydrological methods used to identify zero-flow conditions, and in particular drying events, have limited use when assessing large areas dominated by low-order streams. We developed a novel multimetric index to recognise antecedent stream drying based on the analysis of benthic macroinvertebrate communities. The data used to develop the index were collected in pristine streams with different flow permanence regimes between 2012 and 2014, using standard sampling methods for ecological status assessment. The data include 64 perennial, 19 near-perennial and 27 intermittent benthic macroinvertebrate samples. Metrics considered for the index included variables based on (i) the occurrence of indicator taxa, (ii) the proportion of biological and ecological traits, and (iii) structural community metrics. Linear discriminant analysis identified the metric combinations that best discriminated among the three flow permanence categories. Different metrics were used in the final multimetric index calculation for the autumn and spring season that followed stream drying. In both seasons, the index included the proportion of indicator taxa and the proportion of taxa with high body flexibility. In addition, the autumn index included the proportion of taxa with a preference for organic substrates, whereas in spring the index included total abundance. Independent data from regulatory monitoring activity were used to validate the accuracy of the index. The correct classification of independent samples was 92% and 96% for samples from perennial and non-perennial sites, respectively. The index can be calculated using data collected by routine monitoring programmes used to assess ecological status and provides information about stream intermittence where conventional hydrological monitoring is limited. As intermittent streams increase in extent in global regions including Central Europe, the tool may be of particular interest to those who use invertebrates to monitor or manage these ecosystems.