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 9 cm2 surface on five 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 five 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
