Göksu Delta is an important wetland where the Göksu River reaches to sea in the eastern of the town Tasucu-Ice1. The delta is classified as a Wetland of International Importance according to the Ramsar Convention on Wetlands of International Importance. The amount of fertilizers used in this area was 7200 tons in 2006. These pollutants affect the surface and groundwater quality negatively. The intensively used fertilizers and pesticides contain not only N-and P compounds but also some heavy metals. The contents of all pollutants in surface waters were determined for four different seasons between 2006 and 2008 and with these data a Geographic Information System (GIS) has been constructed by using Map Info. From the photometric heavy metal analysis, it is inferred that the excess concentration of Fe, Ni, Mn, Mo and Cu at some locations is the cause of undesirable quality for drinking purposes. The source of excess concentration of various heavy metals is the agricultural activities and fertilizers. It is determined that in all periods between 2006 and 2008 the heavy metals and other pollutants in the fertilizers and pesticides transported easily to river water with irrigation return flow. The organic pollutants, including COD, BOD, NH 3 and NO 3 followed the sharply increasing trends from Silifke city to Mediterranean Sea. The water quality of Göksu River is modeled and determined that the waste water discharge of 10,700 m 3 /day from Silifke city does not create a serious problem because of the high amount of flow rate of Göksu River.