We assess the recovery of UK lakes from acidification using the combined data from sediment cores and sediment traps to track changes in diatom assemblages in 11 UK upland lakes from pre-acidification times (prior to ca. 1850 AD) to the present (2008 AD). We projected the data into a Principal Component Analysis (PCA) of diatom assemblage data from 121 low-alkalinity lakes in the UK to show how the floristic composition of the core and trap diatom assemblages for each site has changed through time. The results show that the degree of recovery from acidification varies amongst sites but in all cases its extent is limited when compared with the pre-acidification reference. In most cases the recovery, although usually slight, is characterised by a decline in acid tolerant taxa and a return towards taxa that occurred previously at each respective site. In a few cases, however, the floristic composition of recent samples is different from those that occurred during and before the acidification phase. The reasons for this are not yet clear but it is possible that nutrient enrichment from atmospheric N deposition and/or climate change is beginning to play a role in driving water quality as acidity decreases. More generally the results show that annually recovered samples from sediment traps can be successfully combined with sediment core data to provide a continuous record of environmental change in lake systems, and that diatoms collected in sediment traps can be used to provide a very powerful lake monitoring tool.