We evaluated long-term impact of agro-ecological zones and cropping systems on stock and stability of organic C in soils along depth. Sixty geo-referenced soil samples were collected from Terai (TZ) and New Alluvial (NAZ) agro-ecological zones of Wet Bengal. In each zone, soil samples were drawn at 0−0.3, 0.3−0.6 and 0.6−0.9 m depth from rice-potato-jute (R-P-J), rice-vegetables-vegetables (R-V-V), vegetables-vegetables-vegetables (V-V-V) and rice-rice (R-R) cropping systems. Total organic C (TOC) in soils and its pools viz., easily oxidizable Walkley and Black C (CWB), very labile (CVL), labile (CL), less labile (CLL), non-labile (CNL), active (CAP), and passive (CPP) were measured separating on the basis of ease of oxidation with chromic acid for computing different indices of soil organic C (SOC). Among the cropping systems, on average, rice-based systems had higher TOC and CNL than non-rice (V-V-V) one, particularly in NAZ; while non-rice system had a higher per cent allocation of SOC in CVL. Again, a greater per cent of SOC occurred in CPP and CAP under rice-based and non-rice systems, respectively. Anaerobiosis thus facilitated formation of a higher proportion of SOC in recalcitrant pools. Stratification ratios of organic C were higher for soils under NAZ than those under TZ, and also for soils under rice-based systems than those under non-rice one indicating a better soil quality in the former than the latter zone and systems. This was again corroborated with higher values of carbon management index for NAZ than TZ and R-R than V-V-V systems. Further, the recalcitrant indices (RIs) of SOC were higher for soils of TZ than those of NAZ, contrary to the values of lability index (LI). Among the cropping systems, V-V-V had the highest LI values followed by R-V-V > R-P-J = R-R. Along depth, the values of RIs increased, but LI decreased. There was thus an overriding influence of rice and its ecology on the stock and stability of SOC masking the influence of its companion crops in rice-based systems. Therefore, rice-based systems, grown by default in many regions, had a better C economy in soils of this sub-tropical part of the world.