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Abstract. Inner Ambon Bay has been used as a location for fish farming. The mean seasonal of chemical parameters as much as 3,92 – 6,52 ppm for dissolved oxygen, the surface concentration of nitrate and phosphate each one is 0,05 – 0,143 ppm and 0,014 – 0,6 ppm, meanwhile the pH reach 7,95 – 8,44. The mean seasonal of physical parameters about 30,3 – 34,4 ‰ for salinity and the value of surface temperature is 26,5 – 31,5 °C. This research reviews the condition of an ecosystem in Inner Ambon Bay, consist of nutrients, phytoplankton, zooplankton, and detritus (NPZD) concentrations. The input model uses data on temperature and average nitrate concentration from Ambon Marine Aquaculture Center (Balai Perikanan Budidaya Laut Ambon) which is located on 3,63529 °S and 128,2312 °E. Model simulation is carried out for 4 years (2015 – 2018) with a time step of 6 minutes. The model simulation result shows that the mean nutrient concentration is 3,52 – 3,84 mmolC/m3. The verification of nutrient concentration from a model with observation data (nitrate concentration) used a statistics method. The value of RMSE is 0,05 mg/L or 0,5 mmolC/m3, meanwhile correlation is 0,41. The highest nutrient concentration occurred in the east season. It could be influenced by upwelling from Banda Sea that carried high nutrients from the surface.