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Benthic algae are widely used as ecological indicators of the ecological status of streams because they are widely distributed, they show high species diversity and they respond rapidly to human pressures in particular eutrophication and organic pollution. Recent findings have highlighted that in addition to human pressures, alkalinity may also play a role for community composition as bicarbonate becomes an increasingly important carbon source for photosynthesis when alkalinity increases. With this study, we aimed to elucidate how alkalinity influences the distribution of diatoms in Danish lowland streams, and to explore ifdiatom assemblage patterns can be affected by alkalinity in a way that interferes with the ecological assessment using diatom-based indices. We found that alkalinity affect the benthic algae community in lowland streams and that different species of diatoms were associated with different levels of alkalinity, a finding that might indicate dissimilarities in the efficiency of their HCO 3 - use. Nitzschia intermedia, Synedra acus, Nitzschia recta, Diatoma tenue, and Nitzschia linearis were associated with high alkalinity, whereas Synedra rumpens, Fragilaria vaucheriae, Psammothidium bioretii, and Gomphonema parvulum were associated with low alkalinity in streams with very low levels of phosphate. We also found that the Danish indicator for ecological status in streams (a combination of two Austrian indices, the Saprobic Index (SID) and the Trophic Index (TID) may exceed levels acceptable for good ecological status in moderate to high alkaline streams despite low phosphate levels. These findings highlight the need for the development of a diagnostic method to disentangle the effects of alkalinity from eutrophication and, additionally, that we need more insight into the autecology of species to interpret ecological assessments to be able to guide management efforts., Competing Interests: Declaration of competing interest The Authors declare that they have no known competing financial interests r personal relationships that might have influenced the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)