The diatoms assemblage that colonized artificial substrata in the rhithron area of Medellin river was studied. This zone is located in the natural reservation “El Alto de San Miguel” between 1,800-2,800 m. From January to March 1998, were weekly taken samples with the purpose to evaluated variations in the composition of the assemblage under drought stress caused by the ENSO. During the colonization process, 37 diatom species with tropical, subtropical, and cosmopolitan distribution were found. The taxa were grouped in 10 families and 18 genera, being the Naviculaceae that presented the greatest number of genera (6). Spatial and temporal differences were found in diversity and evenness, associated with fluctuations inflow, soluble reactive phosphorus, dissolved oxygen, and ammonium nitrogen; this last variable was the only chemical one significant and correlated with the diatom evenness. The flow presented inverse correlation with diversity (r = -0,43; p = 0,035). The other measured variables did not present important fluctuations and showed an independent behavior in relation to the flow and did not present any relation with the biological indices.