In order to determine the water quality of the Mert Stream, algal indicators and some biological indices (TDI, IDG, PTI, Palmer, DAIpo) based on phytoplankton species were used. Phytoplankton samples were performed monthly from six different sites at a depth of 0.5 meter using a one-litre water sampler between July 2011 and June 2012. After phytoplankton samples were placed in 250-mL dark bottles and fixed with Lugol’s solution until processed in the laboratory, they were identified and counted in the tubular plankton counting chambers using an inverted microscope according to Utermöhl method. Bacillariophyta members became the dominant division in the phytoplankton with an abundance rate of 83.3% and 71 taxa. Lindavia glomerata, Navicula cryptocephala, Cyclotella planctonica, and Navicula veneta were determined as the most dominant species among phytoplanktonic taxa of Mert Stream. Trophic diatom index (TDI) and Generic diatom index (IDG) based on planktonic diatoms were used to determine the trophic status of the Mert Stream. Pollution tolerance index (PTI), Diatom assemblage index (DAIPo) and Palmer index were also included to assess the organic load-based sabrobity level of the Mert Stream. According to the results of mean TDI and IDG (55 and 13, respectively), the trophic status of the Mert Stream is a mesotrophic structure with moderate nutrients and good water transparency. According to the average PTI result (2.7), Mert Stream is in the β-mesosaprobic class, which corresponds to moderate pollution. Considering DAIpo indice, the saprobity of Mert stream is α-oligosaprobic level and the stream is not exposed to a serious organic-based pollution. However, according to the Palmer index, all stations of the Mert Stream except the 6th station are under the threat of high organic pollution. In present study, it was seen that the best biological index that reflects the station-based trophic structure of the stream is IDG, and the best biological index that reflects the station-based organic pollution of the stream is PTI.