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Ecosystem metabolism is a key ecological attribute and easy to describe, but quantifying metabolism in estuaries is challenging. Properly scaling measurements through time and space requires consideration of hydrodynamics and mixing water from heterogeneous sources, making any estimation uncertain. Here, we compared three methods for modeling ecosystem metabolism in a portion of the Sacramento-San Joaquin Delta. Metabolism estimates based on laboratory incubations, continuous in situ buoys, and an oxygen isotope approach all indicated the system was net heterotrophic, and calculated rates were comparable in magnitude when averaged over the 2-month study. Daily metabolic rates based on in situ buoys were the most variable, likely due to horizontal and vertical advection and poor portrayal of the dissolved oxygen budget. After temporally averaging in situ buoy estimates or smoothing the dissolved oxygen time series for tidal effects, rates were more comparable to the other methods, which may be necessary to account for tidal advection and unbalanced contributions from subhabitats within the metabolic footprint. Incubation-based rates represent the finest temporal and spatial scale and only account for pelagic processes, which may explain why incubation-based rates were lower than the other two methods. The oxygen isotope method provided temporally and spatially integrated rates that were bracketed by the other two methods and may be a valuable tool in systems matching the model requirements. Because uncertainty arises in each method from a number of assumptions and scaling calculations, the resolution of metabolic rates in estuaries is likely coarser and more variable than in other aquatic ecosystems.

Metabolic stoichiometry predicts that dissolved oxygen (O2 ) and carbon dioxide (CO2 ) in aquatic ecosystems should covary inversely; however, field observations often diverge from theoretical expectations. Here, we propose a suite of metrics describing this O 2 and CO2 decoupling and introduce a conceptual framework for interpreting these metrics within aquatic ecosys- tems. Within this framework, we interpret cross-system patterns of high-frequency O 2 and CO2 measurements in 11 northern lakes and extract emergent insights into the metabolic behavior and the simultaneous roles of chemical and physical forcing in shaping ecosystem processes. This approach leverages the power of high-frequency paired O 2–CO2 measurements, and yields a novel, integrative aquatic system typology which can also be applicable more broadly to streams and rivers, wetlands and marine systems. This study evolved from discussions during the “Coupling of O 2 and CO 2 dynamics in Lakes” working group during the Global Lake Ecological Observatory Network GLEON 16 meeting held in Orford, Canada in 2014. We are especially thankful to P. Staehr, M. Head, T. Rasilo, S. Bartlett, R.-M. Couture, D. da Motta Marques, T. Kratz, R. Maranger, D. Tonetta, P. Meison, and T. DelSontro who also participated to this working group and B. Obrador for providing useful suggestions which improved the study. We thank Erik Geibrink and Anders Jonsson for help with data acquisition in the Swedish lakes, which was supported by Formas (Grant 210-2012-1461) and Kempestiftelserna (Grant SMK- 1240). We thank the Ontario Ministry of the Environment, Conservation and Parks (formerly Environment and Climate Change) for funding the Harp Lake initiative and Chris McConnell and Tim Field of the Dorset Environmental Science Centre for help in data collection and curation. Work within Buffalo Pound Lake was supported by instrumentation from the Canada Foundation for Innovation, a National Science and Engineering Council Strategic Project Grant, and support of the Saskatchewan Water Security Agency and Buffalo Pound Water Treat- ment Plant. We thank Jay Bauer, Katy Nugent, and others for technical support in Buffalo Pound Lake. S.S. was supported through a post- doctoral fellowship from the National Science Foundation (EAR- 1249769). Financial support for G.A.W. was received from the Swedish Research Council (Grant 2016-04153) and from the Knut and Alice Wallenberg Foundation (Grant KAW 2013.0091). A.L. was supported by Estonian Research Council Grant PSG 32 and IUT 21-2 of the Estonian Ministry of Education and Research. D.V. was supported by postdoctoral fellowships from NSERC and the Knut and Alice Wallenberg Foundation. M.J.B. was supported by postdoctoral fellowships from NSERC and the Delta Stewardship Council Delta Science Program. This study evolved from discussions during the “Coupling of O 2 and CO 2 dynamics in Lakes” working group during the Global Lake Ecological Observatory Network GLEON 16 meeting held in Orford, Canada in 2014. We are especially thankful to P. Staehr, M. Head, T. Rasilo, S. Bartlett, R.-M. Couture, D. da Motta Marques, T. Kratz, R. Maranger, D. Tonetta, P. Meison, and T. DelSontro who also participated to this working group and B. Obrador for providing useful suggestions which improved the study. We thank Erik Geibrink and Anders Jonsson for help with data acquisition in the Swedish lakes, which was supported by Formas (Grant 210-2012-1461) and Kempestiftelserna (Grant SMK- 1240). We thank the Ontario Ministry of the Environment, Conservation and Parks (formerly Environment and Climate Change) for funding the Harp Lake initiative and Chris McConnell and Tim Field of the Dorset Environmental Science Centre for help in data collection and curation. Work within Buffalo Pound Lake was supported by instrumentation from the Canada Foundation for Innovation, a National Science and Engineering Council Strategic Project Grant, and support of the Saskatchewan Water Security Agency and Buffalo Pound Water Treat- ment Plant. We thank Jay Bauer, Katy Nugent, and others for technical support in Buffalo Pound Lake. S.S. was supported through a post- doctoral fellowship from the National Science Foundation (EAR- 1249769). Financial support for G.A.W. was received from the Swedish Research Council (Grant 2016-04153) and from the Knut and Alice Wallenberg Foundation (Grant KAW 2013.0091). A.L. was supported by Estonian Research Council Grant PSG 32 and IUT 21-2 of the Estonian Ministry of Education and Research. D.V. was supported by postdoctoral fellowships from NSERC and the Knut and Alice Wallenberg Foundation. M.J.B. was supported by postdoctoral fellowships from NSERC and the Delta Stewardship Council Delta Science Program.