[This dataset is embargoed until July 1, 2026]. This dataset provides diatom taxon abundance data from 12 rivers in the Cordillera Vilcanota 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, then averaged across the 5 replicates for each site. Data were collected from 11/09/2019 to 18/09/2019. Full details about this dataset can be found at https://doi.org/10.5285/1ef65c7e-08d6-4148-b751-ae106346e091