Abstract The net surface energy flux is computed as a residual of the energy budget using top-of-atmosphere radiation combined with the divergence of the column-integrated atmospheric energy transports, and then used with the vertically integrated ocean heat content tendencies to compute the ocean meridional heat transports (MHTs). The mean annual cycles and 12-month running mean MHTs as a function of latitude are presented for 2000–16. Effects of the Indonesian Throughflow (ITF), associated with a net volume flow around Australia accompanied by a heat transport, are fully included. Because the ITF-related flow necessitates a return current northward in the Tasman Sea that relaxes during El Niño, the reduced ITF during El Niño may contribute to warming in the south Tasman Sea by allowing the East Australian Current to push farther south even as it gains volume from the tropical waters not flowing through the ITF. Although evident in 2015/16, when a major marine heat wave occurred, these effects can be overwhelmed by changes in the atmospheric circulation. Large interannual MHT variability in the Pacific is 4 times that of the Atlantic. Strong relationships reveal influences from the southern subtropics on ENSO for this period. At the equator, northward ocean MHT arises mainly in the Atlantic (0.75 PW), offset by the Pacific (−0.33 PW) and Indian Oceans (−0.20 PW) while the atmosphere transports energy southward (−0.35 PW). The net equatorial MHT southward (−0.18 PW) is enhanced by −0.1 PW that contributes to the greater warming of the southern (vs northern) oceans.