[This dataset is embargoed until July 1, 2026]. This dataset provides diatom taxon abundance data from 11 rivers in the Cordillera Blanca region of the Peruvian Andes. Benthic diatoms were collected from a 9cm2 surface on 5 submerged cobbles at each river site. Diatoms were identified and abundances determined using microscopy methods in the laboratory from each replicate, then averaged across the 5 replicates for each site. Data were collected from 7/05/2020 to 16/05/2020. Full details about this dataset can be found at https://doi.org/10.5285/6f8b326e-d1f0-413e-b8ac-472b83c7de5e