Non-point source (NPS) modeling requires a vast amount of diverse data for simulation of watershed processes. The data gathering process in developing countries is a challenging task because of data scarcity and reliability, gaps in available data, and data suitability as model input together with temporal and spatial availability of data. A Model Support System (MSS) encompasses the entirety of the processes which precede the simulations. This study documents the concepts of MSS and modeling project management cycle, and defines a pathway on how the modeling efforts should be organized towards an integrated watershed management goal. It emphasizes that in the developing countries, establishing an MSS for rural NPS modeling is almost as challenging as developing a calibrated and validated model. An MSS based on difficulties, and workarounds bound to local conditions for the Koycegiz-Dalyan watershed located in Turkey is presented as a case study. Moreover, Hydrological Simulation Program-Fortran (HSPF) is executed by the gathered and derived data, which produced acceptably positive results. A stepwise documentation on how to initiate and proceed with a project for "non-point source modeling" is made available for use of decision-makers, researchers and modelers to replicate these studies on other sensitive watersheds of Turkey or to expand these efforts by filling necessary research/resource gaps highlighted by this study.