Kucukcekmece Lagoon in Istanbul (Turkey) receives increasing attention due to its deteriorating water quality and the pollution of the surrounding watershed. In this study, seven sampling points were selected and environmental parameters including lagoon water (pH, electrolytic conductivity), sediment and soil of the littoral zone (pH, electrolytic conductivity, texture, shell content, total carbon and nitrogen concentrations) were measured and the effects of high salinity on the total C, total N, and C/N ratio in different organs of Phragmites australis were discussed. According to the electrolytic conductivity results, our sampling sites can be considered as highly saline environments. Texture analyses have indicated that the sediment and soil samples were mostly sandy with a high sensitivity to pollution discharges. Highest N concentrations were measured in the leaves of Phragmites with an increasing order in the urban, agricultural and industrial sampling sites (1.73-3.29%). N inputs into the highly saline Kucukcekmece Lagoon can be associated with different pollution sources and the observed Phragmites australis stands may be favourable for the natural elimination of N in this area.