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This research aims to develop a decision support system based on the conservation of biotopes within a Mediterranean agricultural landscape through the optimization of agricultural productivity. The first stage of this research includes mapping crop patterns using medium-resolution satellite sensor data recorded by LANDSAT and Sentinel-2 over Lower Seyhan Plain (LSP) located at the Eastern Mediterranean coast of Turkey between 2010 and 2016. In the second stage, crop productivity of three major crops namely winter wheat, corn, and cotton derived from image classification was modelled spatially and temporally through the CropSyst model. Additionally, the model was also revealed irrigation return flow from the drainage and the related N load. In the last stage, conservation principles and policies were recommended to diminish the detrimental impacts of agricultural fertilizer loads to the biotopes through drainage channels. The model results indicated that crop productivity of wheat, cotton, first crop corn, and second crop corn 21%, 28%, 47%, and 4% of total production in LSP, respectively. The average annual crop production of the wetlands region was 161,548 tons and equal to 16,5% of the total plain area. The largest amount of drainage water comes from cotton and second crop corn cultivation; the smallest amount comes from wheat and first crop corn cultivation. The largest amount of nitrogen remaining within the system was from second-crop corn, whereas, the smallest amount from wheat. It can be concluded that nitrogen fertilizer should be applied according to the soil characteristics, reduced by 5% for wheat, 10% for first crop corn, and 50% for second crop corn. As a result of this reduction fertilizer uptake efficiency will increase and N load to the wetlands will decrease.