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The aim of this paper is to determine and compare the environmental factors controlling longitudinal colonisation of periphytic algae in agricultural and urbanization effects of a lowland river, the Tundzha River, located in Turkish Tunca. To investigate the effect of the environmental factors on periphyton colonization at the river, 6 stations were selected and samples were collected between April 2012 and March 2013. Canonical correspondence analyses have been applied to clarify relationships between environmental variables and periphytic algae. During the study, the Shannon-Wiener diversity index (H′) varied from 1.62 to 3.91. The phytoplankton biovolume was positively related to pH, temperature, salinity, chlorophyll- a and nutrients, and was negatively correlated with dissolved oxygen, turbidity, and silicate. Out of the 5 divisions and of 73 identified species of phytoplankton, the diatoms, namely Fragilaria ulna, Cymbella tumida, Cocconeis placentula, Gomphonema acuminatum and Cymbella cystula were found to be dominant. In addition to these species, the biovolumes of filamentous diatom Melosira varians, filamentous blue-green algae Oscillatoria limosa, and placcoderm desmids Cosmarium botrytis were determined to be at high levels during the year. The euglenoid blooms in St.5 showed many times during the study period.