The tropical eastern Indian Ocean (TEIO) is characterized by complex seasonal circulation and high sensitivity to Indian Ocean Dipole (IOD) variability. Here, shipboard observations from spring 2012, autumn 2013, and autumn 2016 are synthesized to examine how multilayer circulation and an extreme negative IOD (nIOD) regulated hydrography, subsurface chlorophyll-a, oxygen, and nutrient distributions. Under background conditions, the Wyrtki Jets, Equatorial Undercurrent, Equatorial Intermediate Current, and Antarctic Intermediate Water jointly shaped the depth and intensity of the subsurface chlorophyll maximum (SCM) and the vertical structure of two oxygen-minimum layers. During the 2016 nIOD, anomalous westerlies and an intensified Wyrtki Jet generated eastward convergence and downwelling Kelvin-wave forcing, deepening the thermocline and strengthening upper-ocean stratification. These changes suppressed upward nutrient transport, displaced and weakened the SCM, and altered subsurface circulation pathways. Meanwhile, rainfall-related nitrogen inputs and oxygen depletion in poorly ventilated waters modified nutrient stoichiometry. Covariation among dissolved oxygen, pH, and dissolved inorganic carbon further indicated remineralization-driven deoxygenation and localized acidification. These findings demonstrate how background circulation preconditions the biogeochemical response of the TEIO to extreme IOD forcing.