The meridional circulation and transports at 30°S in the Pacific and Indian Oceans for the years 2002–2003 and 2009 are compared, using GO-SHIP hydrographic section data with an inverse box model and several choices of constraints. Southward heat transport across the combined Indian-Pacific sections, reflecting net heating north of these sections, doubled from −0.7±0.2 PW in 2002–2003 to −1.4±0.1 PW in 2009 (negative sign is southward), with the increase concentrated in the Indian Ocean (∼0.6 PW compared with ∼0.2 PW in the Pacific), and was insensitive to model choices for the Indonesian Throughflow. Diagnosed net evaporation also more than doubled in the Indian Ocean, from 0.21–0.27Sv in 2002–2003 to 0.51–0.58 in 2009, with a smaller but significant increase in net evaporation in the Pacific, from 0.06–0.08Sv to 0.16–0.32Sv. These increased heat and freshwater exports coincided with Indian Ocean warming, a shift in the Indian’s shallow gyre overturning transport to lower densities, and an increase in southward Agulhas Current transport from 75Sv in 2002 to 92Sv in 2009. The Indian’s deep overturn weakened from about 11Sv in 2002 to 7Sv in 2009. In contrast, the Pacific Ocean overturning circulation was nearly unchanged from 2003 to 2009, independent of model within the uncertainties. The East Australian Current transport decreased only slightly, from −52Sv to −46Sv.The southward Pacific Deep Water transport was at a higher density than the southward Indian Deep Water transport in both years and all models, similar to prior results. Estimated diapycnal diffusivity and velocity are strongly enhanced near the ocean bottom and are higher farther up in the water column in the Indian than in the Pacific, likely extending the reach of Indian Ocean overturning up to shallower depths than in the Pacific.The horizontal distribution of transports in the Pacific at all depths changed notably from 2003 to 2009, despite the stability of its meridional overturning structure. The 2009 horizontal structure resembles a “bowed gyre”; the hydrographic section data show that this disturbance extends to the abyss and disrupts the Deep Western Boundary Current structure in the Southwest Pacific Basin. Satellite altimetry suggests association with slow westward Rossby wave propagation generated in the eastern Pacific, with no apparent effect on the net overturning circulation.The Indian Ocean’s upper ocean horizontal structure was stable between the two years even though its shallow gyre overturning transports changed significantly. On the other hand, northward abyssal transports concentrated in the central Indian Ocean (Crozet Basin) in 2002 shifted westward to the Mozambique and Madagascar Basins in 2009, although the Crozet Basin’s Deep Western Boundary Current existed in both years.