An in situ experiment determined that the addition of ammonia N-NH 4 + , nitrate N-NO 3 – and phosphate P-PO 4 3– to an oligotrophic Andean stream significantly affected diatom composition and diversity. Over a nine-month period, fertilized and non-fertilized sections of the stream were studied for their environmental characteristics and diatom composition. Nutrient concentrations were increased three times in a downstream section with respect to those occurring naturally upstream. Alpha diversity (Shannon-Wiener [H”] and Simpson [S] indices) were determined monthly. In the non-fertilized control section, diatom diversity was significantly ( p ≤ 0.05) related to water flow and P and N concentrations. In the fertilized section diversity was associated to the enhanced ammonia and phosphorus. A redundancy analysis (RDA) showed that conductivity, water flow and nutrient concentrations contributed to the diatom assemblage composition (83% along the first two axes). Achnanthidium minutissimum, Cocconeis placentula , and Epithemia sorex occurrence was related to low phosphorus concentration . Epithemia adnata var. minor , Nitzschia dissipata , and Reimeria sinuata were associated with high P concentrations, high water flow and low conductivity Navicula rynchocephala , Gomphonema parvulum , Navicula capitatoradiata , and Melosira varians were associated with high P.