Abstract The Flores Sea, Java, and Makassar Strait are areas where water masses meet as well as one of the entry points for the Indonesian Through Flow. Freshwater mass from the Pacific Ocean enters Indonesian waters through the Makassar Strait. Not only that, Indonesia’s maritime region is influenced by the Asian-Australian Monsoon, which also causes seasonal changes in temperature and salinity. This phenomenon affects primary productivity in Indonesian waters as indicated by variations in chlorophyll-a concentrations in surface waters. Therefore, it is important to study the dynamics of chlorophyll-a in time series to better understand the ecosystem and the phenomena that occur. This study aimed to analyze the spatio-temporal variation of chlorophyll-a in the waters surrounding the Flores Sea, Java, and Makassar Strait, and its correlation with temperature and salinity over a period of seven years, from 2016 to 2023. This reasearch uses chlorophyll-a data collected from sensor, named Ocean and Land Color Instrument carried by the Sentinel-3 satellite. The chlorophyll-a data used is Ocean Color 4 for MERIS data. This study found that chlorophyll-a concentrations in the Flores Sea, Java, and Makassar Strait sample areas tend to be high during the Northwest Monsoon period, along with the arrival of the rainy season which increases river water runoff. On the other hand, chlorophyll-a concentrations in the southern waters of Java to Nusa Tenggara exhibit a notable increase during the Southeast Monsoon, which is subsequently accompanied by a decline in temperature of sea surface and a rise in salinity of sea surface. In 2018 and 2019, the occurrence of the El Niño phenomenon, along with the positive phase of the IOD, led to an increase in chlorophyll-a. From 2018 to 2019, the average chlorophyll-a reached 0.71 mg/m3 in the Flores Sea and Makassar Strait and 0.73 mg/m3 in the Java Sea. This study analyzes chl-a based on satellite observation data that may have errors due to cloud cover. Further research with in situ observation methods is needed for better results and a longer temporal range so that the variability of chl-a against the global phenomena of ENSO and IOD can be seen more clearly.
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