In a changing ocean, tropical waters can be instructive as to the potential effects of climate induced changes on marine ecosystem structure and function. We describe the relationships between planktonic community respiration (CR), net community production (NCP), gross primary production (GPP), and environmental variables in 14 regions and three ecosystem types (coastal, coral reef, and open sea) from Australia, Papua New Guinea, and Indonesia. The data are compiled from separate studies conducted between 2002 and 2014 with the goal of better parameterizing the metabolic balance in tropical marine waters. Overall, these regions were strongly autotrophic (average GPP:CR ratio: 2.14 ± 0.98), though our dataset of 783 paired measurements did include some oceanic stations where heterotrophy (GPP:CR < 1) was predominant, and some coastal stations that were intermittently heterotrophic. Our statistical analysis suggested that temperature was the most important determinant of CR in coral reef and ocean ecosystems but less so in coastal ecosystems, where chlorophyll concentration was more important. In contrast, chlorophyll and sampling depth were more important in regulating GPP than temperature. The relationships between temperatures and metabolic rates showed that these were ecosystem-dependent, with coastal ecosystems showing less response to temperature than coral reef and open sea sites. The threshold of GPP to achieve metabolic balance fell in a range between 0.715 mmol O 2 m −3 d −1 in the Coral Sea to 10.052 mmol O 2 m −3 d −1 in mangrove waterways of Hinchinbrook Channel. These data allow regions in and around northern Australia to be ranked in terms of trophic state, ranging from the oligotrophic Scott Reef (GPP:CR = 0.84 ± 0.08) to productive surface waters of the Kimberley coast (GPP:CR = 5.21 ± 0.62). The measurement of pelagic metabolism shows potential as a quantitative tool to monitor the trophic state of coastal waters.