Freshwater acidification continues to be a major problem affecting large areas of Europe, and while there is evidence for chemical recovery, similar evidence for biological recovery of freshwaters is sparse. The need for a methodology to identify waterbodies impacted acidification and to assess the extent of biological recovery is relevant to the EU Water Framework Directive, which requires methods to quantify differences in biology between impacted and unimpacted or reference sites. This study presents a new WFD-compliant metric based on diatoms (Diatom Acidification Metric: DAM) for assessing the acidification status of rivers. A database of 558 benthic diatom samples and associated water chemistry data was assembled. Diatom taxa were assigned to one of 5 indicator classes on the basis of their pH optimum, assessed using Gaussian logistic regression, and these indicator values used to calculate a DAM score for each site using weighted averaging. Reference sites were selected on the basis of their acid neutralising capacity (ANC) and calcium concentration, and a regression model developed to predict expected DAM for each site using pH and total organic carbon (TOC) concentration. Site-specific DAM scores were used to calculate ecological quality ratios ranging from ≥1, where the diatom assemblage showed no impact, to (theoretically) 0, when the diatom assemblage was indicative of major anthropogenic activities. The boundary between ‘high’ and ‘good’ status was defined as the 25th percentile of Ecological Quality Ratios (EQRs) of all reference sites. The boundary between ‘good’ and ‘moderate’ status was set at the point at which nutrient-sensitive and nutrient-tolerant taxa were present in equal relative abundance. The methodology was evaluated using long-term data from 11 sites from the UK Uplands Waters Monitoring Network and is shown to perform well in discriminating naturally acid from acidified sites.