The tolerance of ten diatom species (Bacillariophyceae) to water's physico-chemical factors in the Sarapiqui River, Costa Rica. Benthic diatoms are the periphyton component most studied in Costa Rican rivers, yet there is still much to be known about their ecology. This study aims to contribute to this knowledge. Periphyton samples from six locations along the middle reach of Sarapiquí river and some of its tributaries were taken and analyzed from 2010 to 2012. A total count of 400 frustules was performed in each sample to obtain relative abundances of each species. Ten species, which were easily recognized at the light microscope, were analyzed here: Achnanthidium exiguum, Coconneis placentula, Cymbella tumida, Luticola goeppertiana, Luticola ventricosa, Navicula symmetrica, Nitzchia clausii, Nupela praecipua, Reimeria sinuata and Synedra goulardi. Their abundance was related to physico chemical data at each site for every sampling date (dissolved oxygen, temperature, conductivity, total suspended solids, turbidity, pH and alkalinity) with a canonical correspondence analysis (CCA) that allowed distinguishing three sectors along the river according to altitude. These sectors differed by substrate, riparian vegetation cover, and physic-chemical parameters, all of which resulted in differences in diatom species composition among them. Optimum values and tolerances form each environmental parameter were calculated for each species. Our results showed that A. exiguum, R. sinuata, L. ventricosa and C. tumida, were dominant in clean and well oxygenated waters with low temperatures. The species N. praecipua, S. goulardi, C. placentula, L. goeppertiana, N. clausii and N. symmetrica inhabited warm waters with high turbidity and low oxygen. The species A. exiguum, R. sinuata were dominant in sites with low alkalinity and conductivity, whereas species like N. symmetrica, C. tumida and L. ventricosa showed a positive relationship with conductivity and pH. The studied species showed good characteristics of their value as water quality indicators, yet due to different interpretations by several authors, it is necessary to perform further studies at more river basins in the country. Rev. Biol. Trop. 64 (1): 105-115. Epub 2016 March 01.