Reuse of drainage water for crop production is a common practice in downstream section of the Lower Seyhan Irrigation Project area in the Mediterranean region of Turkey. Therefore, effective salinity control measures must be implemented for sustainable irrigated agriculture, which requires safe use of saline, low quality irrigation and drainage waters for crop production. A five-year study was conducted in the Lower Seyhan Irrigation Scheme from 1991 to 1996 in order to evaluate the response of cotton and wheat grown on a clay soil in a sequence to drainage water applications with different leaching fractions as well as salinity build-up in the soil profile during each growing season in Tarsus. Effect of winter rainfall on salt balance of the soil profile was investigated. In addition, water quality changes occurred in drainage canal were evaluated throughout the study period.