The waters that surround the Indonesian archipelago are home to some of the most fruitful primary resources that can be found anywhere in the southeastern Indian Ocean. In this work, we present an investigation of seasonal fluctuations in nutrient content within the region, utilizing 30-years reanalysis data generated by Copernicus Marine Service. The month of SON exhibits the maximum concentration of nitrate content, primarily observed in the southern region of Java and the Lombok Strait. The concentrations of nitrates experience significant changes that are notably impacted by Indian Ocean Dipole (IOD) occurrences. Specifically, a positive IOD event is associated with elevated nitrate levels, particularly during the period spanning from June to December. Furthermore, in the southern Java region, an inverse correlation was identified between nitrate concentrations and surface zonal currents, commonly referred to as the South Java Current (SJC). Concurrently, the reinforcement of the Indonesian Throughflow (ITF) in the Lombok Strait is consistently accompanied by an elevation in nitrate concentration within the southern region.