Algae are among the key organisms of aquatic ecosystems. While there have been a large number of important algological studies on different river basins in Turkey, the use of algae in biomonitoring is a new approach. Epiphytic and epilithic algae in the Melen River were studied between May 2003 and April 2004. A total of 148 taxa, with 101 belonging to Bacillariophyta, 18 to Chlorophyta, 9 to Charophyta, 13 to Cyanobacteria, 5 to Euglenophyta, and 2 to Miozoa, were identified in this study. Members of Bacillariophyta were the dominant taxa at all sites, with oligohalobious-indifferents and alkaliphiles being the most common. Among the non-diatom taxa, there were more species with oligohalobious-indifferent and indifferent properties. The river water was alkaline and temperate, with low salinity characters. Bio-indications (autecology) of the river were studied. From the results, organic pollution indicators of Watanabe's classification (46 species, 31.1%) constituted three groups (saproxen, eurysaprobe and saprophile). Based on the classification (according to Watanabe's system) and RPI (River Polluted Index), the ecological conditions of Melen River were assessed as low, with a moderate level of organic pollution, and lightly to moderately polluted, respectively.