For the sustainable management of receiving waters, a unified holistic approach is required. This is why watershed based management is becoming an increasingly popular instrument for the improvement of water quality since the late 1980s. The aim of the study is initializing the components of an integrated modeling system intended to be used for coastal ecological analysis of a lagoon. For attaining this purpose, a general water quality model and a watershed model, which will calculate the nutrient inputs and force the water quality model, are used. The study area was selected as Koycegiz - Dalyan Lagoon, located at the southwest of Turkey along the Mediterranean Sea Coast. The Soil and Water Assessment Tool (SWAT) was used as the watershed model to estimate the non-point pollutant loads arising from the study area, and Water Quality Analysis Simulation Program (WASP) was selected for the water quality modeling studies. The flow and the pollutant loads discharging into the Lagoon system from its sub-watersheds were estimated by SWAT. The estimated flow and pollutant load outputs obtained from this model were used as the input to WASP. NH3-N, NO3--N, detrital nitrogen, dissolved organic nitrogen, PO43--P, detrital phosphorus, dissolved organic phosphorus, total phytoplankton, dissolved oxygen, CBOD, detrital carbon and salinity parameters were simulated. The simulation results indicated that WASP was able to catch the general trend of the monitoring data. However, in most cases, the simulation results for the boundaries fitted at a higher level than the other regions of the system.