The study of marine biogeochemical cycling of Mn, a bio-essential trace metal, is crucial to decipher its relative role in controlling the production and diversity of marine phytoplankton. Furthermore, Mn oxides and oxyhydroxides act as sinks for other trace elements in the water column, and Mn redox cycling may exert a major control on the vertical distribution of these elements. Dissolved Mn (dMn) concentrations are measured along two GEOTRACES-India (GI) transects, GI05 and GI10, for a basin-wide investigation of biogeochemical controls on the dMn distribution in the Arabian Sea (AS). Surface dMn distribution shows a strong spatial gradient, with relatively dMn-rich levels in the eastern AS (3.4–5.7 nmol kg−1) compared to the central and western AS (1.2–2.3 nmol kg−1). This correlates with the higher model estimates of soluble Mn input from the atmospheric dust deposition in the eastern AS (∼1.5–2.0 times of input in the western and central AS), and probable additional Mn input from riverine discharge and shallow shelf region of the eastern AS. In the south-eastern AS, a correlated increase in surface dMn with a decrease in salinity indicates the Mn input by the advection of dMn-rich, low-salinity Bay of Bengal (BoB) surface waters to the AS under the influence of the Northeast Monsoon Current. Our mass balance estimates for dMn in the euphotic waters (upper 100 m) suggest important contributions from atmospheric Mn deposition (14–99% of the total estimated input flux), and dMn input/dilution (13–74% of the total estimated input or removal flux) due to lateral/vertical advective-eddy diffusive mixing. Mn-oxidation and passive scavenging are determined to be the dominant processes for the dMn removal (61–99%) from the euphotic zone (upper 100 m), while export via Mn bio-assimilation is comparatively negligible.In the AS denitrification zone, the observed dMn maxima in the upper thermocline depths (∼200–400 m) result from the in situ reductive dissolution of Mn oxides and oxyhydroxides, and lateral advective-eddy diffusive Mn flux from the reducing sediments of the western Indian margin. Outside the denitrification zone, in the northern and western AS, a shift of dMn maxima to the lower thermocline waters (∼500 m) indicates the change in the source region and dMn input from the reducing margins of the north (Pakistan Margin) and north-western AS (Oman Margin), intersecting the core of the oxygen minima at the depth range of 400–600 m.Deep water (>1500 m) dMn concentrations are low (<0.3 nmol kg−1) in most of the AS regions. Anomalous dMn enrichment in the deep waters is observed in the southern and western AS, presumably indicating the influence of hydrothermal plumes emanating from the active hydrothermal vents over the Carlsberg Ridge and spreading ridges in the Gulf of Aden. A correlated and localized increase in dMn and dAl levels close to the Murray Ridge hints at dMn input from the sediment resuspension over the ridge and subsequent Mn dissolution in low-oxygen waters (DO < 20 µM) and/or diffusive flux from the Mn-rich pore waters.