Climate change severely affects the third-largest maritime regions, disrupting physical and biogeochemical processes and Ocean Net Primary Productivity (NPP), which affects the marine food web, fisheries, and livelihoods of surrounding regions. This study examined changes in NPP in the Indian Ocean and its drivers. The Ocean warming, equatorial and Pacific warm pools, stratification fluctuations, circulation changes, nutrient transport, monsoons, and different seasonal processes significantly influenced these microbial mats. The Copernicus Marine Environment Monitoring Service (CMEMS) reanalysis data shows a high declining NPP trend in the Indian Ocean (-0.85 mgC/m3/day/yr). The high warming rate (0.01–0.02 °C/yr) primarily drives regional NPP alterations. The causal discovery analysis shows that sea surface temperature (SST) provides high negative feedback to NPP during all-time delays. Nitrate and phosphate show a positive association, reinforcing positive feedback, and Redfield stoichiometry holds paramount significance in fostering the NPP. Negative feedback is observed from the Western Pacific Index (WP), Oceanic Niño Index (ONI), Multivariate ENSO Index (MEI), and Pacific Decadal Oscillation (PDO). This climate pattern can modify mesoscale atmospheric circulation, influence currents, and change temperature and nutrient availability. The positive connection between the Southern Oscillation Index (SOI) and NPP underscores the complex interplay between climate patterns in the region. The Indian Ocean Dipole (IOD) negatively feedbacks the NPP. Various other climate patterns and events indirectly affect IO biogeochemical processes.