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 the 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 southeast season. It could be influenced by upwelling from Banda Sea that carried high nutrients from the surface.

Inner Ambon Bay is used for fishery research by the government. One of the species that has been cultivated is seabass because it has high economic value. Seabass cultivation in floating net cages has been developed by Ambon Marine Aquaculture Institute (BPBL-Ambon). The characteristics of seawater in Inner Ambon Bay (IAB) based on the observation data in the project “Ocean Current System of Indonesia Waters and Its Effect on Marine Fisheries Production” in May 2017 show that the temperature is in the range 29.8 – 30.9 °C. Meanwhile the salinity is about 26.1–31.4 PSU and the chlorophyll concentrations as much as 0.88 – 3.61 mg/m3. The 1D ecosystem model simulation is performed to know how is the growth rate of seabass is with two-way interaction between nutrient, phytoplankton, zooplankton, and detritus (NPZD) towards zooplanktontivor (fishes which consume zooplankton). The verification of model result (fish mass) with the observation data of fish mass which conduct by BPBL Ambon show the RMSE value is 0.001 kg and the correlation is 0.99. The nutrient concentration since 2016 – 2018 in the range of 3.08 – 3.78 mmolC/m3. While the phytoplankton, zooplankton, and detritus concentration during 3 years each one is 4.67 – 5.84, 11.53 – 15.77, and 16.88 – 20.67 mmolC/m3. The fastest growth rate of Seabass with the first scenario is 1.52 grams/day with the duration of 257 days and when the juvenile of seabass spread in January. The fastest growth rate of Seabass with addition feed is 2,23 grams/day during 175 days.

Outer Ambon Bay (TAL) and Inner Ambon Bay (TAD) are part of Ambon Bay, which are semi-enclosed waters bounded by a narrow threshold. The characteristics of TAL are strongly influenced by the condition of the Banda Sea waters. Physical characteristics in the Banda Sea are influenced by the phenomenon of upwelling during the southeast season which brings water masses with high salinity and low temperature into the TAL. The condition of Ambon Bay is also influenced by the density gradient and tidal upwelling phenomenon. A 3-dimensional hydrodynamic modeling simulation was conducted to see the tidal upwelling phenomenon that affects the physical dynamics in Ambon Bay. The model simulation time was adjusted to the southeast season, namely June 1 - October 31, 2015. Comparison of simulated tidal elevation values with observation data showed a Root Mean Square Error (RMSE) value of 0.11 m with a correlation coefficient of 94.3%. The distribution of water temperature from the model simulation shows the same value as the satellite image data, which is 26°C.