The southern waters of the Sumatra‐Java Islands, within the Indo‐Pacific Warm Pool, are highly susceptible to global climate change impacts. Understanding particulate inorganic carbon (PIC) dynamics and environmental responses in this region is critical for assessing climate change effects on marine ecosystems. Utilizing two decades of remote sensing PIC data (2003–2022), we identified five sub‐regions via K‐means clustering: the Sunda Strait, southern coastal/offshore waters of Sumatra Island, and southern coastal/offshore waters of Java Island. Self‐Organizing Map explored interannual PIC variations, while Generalized Additive Models delineated driving factors. In the Sunda Strait, PIC dynamics are influenced by water exchanges between the Indonesian Seas (ISs) and eastern Indian Ocean (EIO). Seasonally, PIC concentrations peak during the east monsoon (boreal summer); decreasing during positive Indian Ocean Dipole (+IOD) and El Niño events. Along the southern Sumatra, PIC variations positively correlate with rainfall and photosynthetically active radiation (PAR). Along the southern Sumatra, upwelling drives PIC variations, with higher concentrations during mature summer monsoon induced upwelling periods. PIC increases during +IOD and decreases during El Niño. Our study highlights the nexus between nutrients, physical factors (e.g., rainfall), and climatic events (e.g., El Niño) on PIC concentrations. Climate‐induced changes in oceanic physical processes modulate nutrient concentrations, thereby governing PIC variations. We propose a mechanistic model to elucidate PIC variations in upwelling areas. Findings suggest that prospective climate variability, encompassing alterations in climate events, rainfall, and temperature, may escalate PIC concentrations within the study area, advocating PIC as a forward‐looking climate change indicator.