Every estuary has a heartbeat, and for the first time scientists have watched one beat across an entire harbor, day and night, for a full year. In a study published in iScience, a team led by Andrew Lohrer of New Zealand’s Institute for Earth Science mapped seafloor primary production across Ōhiwa Harbour, a shallow barrier-enclosed estuary on the east coast of the North Island with a mean depth of roughly two meters. The result is a dynamic portrait of an ecosystem that literally inhales and exhales oxygen with the sun, the tide, and the seasons—a “breathing seascape” whose rhythms had never before been quantified at the scale of a whole estuary.
The challenge the researchers set out to solve is one that has frustrated coastal scientists for decades. Satellites can track ocean productivity in the open sea by detecting the green pigment of phytoplankton, and these observations have transformed our understanding of global carbon cycling and marine food webs. But in shallow, murky estuaries, the algorithms fail. Suspended sediments and colored dissolved organic matter absorb and scatter light in ways that confuse the satellite signal, and in very shallow water the seafloor itself reflects and absorbs light, further muddying the picture. Yet it is precisely these shallow systems where the seafloor matters most: as water depth decreases, the biomass of benthic producers such as microalgae, turfing algae, and seagrass per unit of seabed increases, while the phytoplankton biomass in the water column above that seabed shrinks. In estuaries averaging two meters deep or less, seabed production can account for the majority of the ecosystem’s total primary productivity.
To see past the murk, the team built their model from the ground up, using empirical measurements rather than satellite data. The approach had three pillars. First, they constructed a harbor-specific seabed light model, driven by incident sunlight recorded at a weather station near Whakatane, bathymetry assembled from vessel surveys and LIDAR, and turbidity profiles collected at more than forty locations throughout the harbor. Boosted regression tree models, trained on 1,243 paired measurements of light penetration, depth, and turbidity, predicted the percentage of surface light reaching every ten-by-ten-meter grid cell of the harbor at two-hourly intervals across an entire year, with a mean deviance explained of 0.94. Second, they mapped the distribution of the three dominant seabed habitats: seagrass, sand, and mud. Third, they linked light to life through habitat-specific photosynthesis-irradiance curves derived from aquatic eddy covariance deployments, an instrument technique that measures oxygen exchange between the seafloor and overlying water continuously, at high frequency, over multiple day-night cycles.
Those photosynthesis-irradiance curves revealed striking differences among habitats. Seagrass reached a maximum photosynthetic rate of 183 millimoles of oxygen per square meter per day, five and a half times higher than mud at 33.1 and more than double that of sand at 88.1. But seagrass also consumed oxygen fastest at night, at 72.3 millimoles per square meter per day, compared with 47.6 for sand and 28.6 for mud. Each habitat switched from net oxygen consumption to net production at a different light threshold, known as the compensating irradiance point: mud required the least light, at 23.8 micromoles of photons per square meter per second, sand needed 34.6, and seagrass needed 69.3. These curves, combined with the habitat map and the light model, allowed the researchers to compute net oxygen flux for every grid cell, every two hours, for a full year from June 2020 to May 2021.
The resulting maps are visually arresting. Patches of intertidal seagrass blaze bright green as hotspots of production, while the deeper subtidal channels appear in dark hues even where the sediment type is identical to shallower areas nearby, because light attenuates with depth. When the daily values were averaged across the whole harbor, a clear seasonal rhythm emerged. Winter, from June to August, was the low point, with productivity of 44.7 plus or minus 8.9 millimoles per square meter per day, significantly lower than the other three seasons. Spring averaged 55.9, autumn 53.1, and summer 51.5, none significantly different from one another. The single lowest day fell on June 25, 2020, at 16.7 millimoles per square meter per day, and the highest on September 9, 2020, at 65.1. July was the weakest month overall, averaging 38.6, significantly below every other month.
Perhaps the most remarkable finding is that Ōhiwa Harbour remained net autotrophic—producing more oxygen than it consumed—on every single day of the year, even in the depths of winter when turbidity was highest and sunlight weakest. Monthly average productivity never dropped below 38 millimoles per square meter per day. The researchers attribute this resilience to the harbor’s extreme shallowness: 79 percent of it is intertidal, and the high productivity of shallow seafloor relative to deep water kept the system in the black. Seagrass, despite covering only three percent of the seascape, punched far above its weight, contributing two to five times the productivity of other habitats under high light. The team notes that even though their seagrass curve was built from data collected outside Ōhiwa and in a single season, the harbor-wide patterns are relatively robust to inaccuracies in that curve because seagrass occupies such a small fraction of the domain.
The implications reach well beyond one New Zealand estuary. Estuaries are widely described as among the most productive habitats on Earth, yet whole-estuary productivity dynamics have rarely been mapped, leaving a gap in our ability to protect areas of high ecosystem functioning—a strategic goal of the Kunming-Montreal Global Biodiversity Framework. The stakes are rising. Climate change is expected to increase sediment loads to estuaries through more frequent and intense storms, while sea level rise deepens shallow systems, and together these forces are “darkening” estuarine seabeds, cutting the light that fuels benthic production. Meanwhile, the historical reclamation of shallow intertidal habitats near coastal cities has likely reduced the oxygen-producing capacity of those systems, potentially contributing to the hypoxic zones that have accumulated exponentially worldwide since the 1950s, with consequences ranging from altered biogeochemistry to fish kills and shellfish die-offs.
The study also carries a cultural dimension. The researchers worked alongside Ngāti Awa, the Indigenous Māori guardians of Ōhiwa Harbour, whose restoration efforts recently led to the return of dense beds of green-lipped mussels near the harbor entrance. Māori conceptualize waterways as living beings whose vitality, or mauri, depends on the health of all their parts, much like the organs of a body. The pulsed daily, tidal, and seasonal rhythms of productivity the model revealed resonate directly with this worldview: the seafloor as a breathing lung whose maintenance sustains the whole. The mussel beds themselves illustrate a subtlety of valuation—a dense mussel bed is likely a net oxygen sink because of its enormous animal biomass, yet it delivers food, water purification, and food web support, showing that low seabed production does not mean low value.
The authors are candid about limitations. The model is heuristic rather than strictly predictive: seagrass distribution was a single snapshot in time, sand and mud were treated as homogeneous, intertidal production was assumed to match submerged production at maximum irradiance, and only a quarter of the eddy covariance deployments occurred within Ōhiwa itself, in winter only. With updated habitat layers, the framework could become far more accurate. Even so, the team has provided something coastal managers have lacked: a transferable tool, with code publicly available on Figshare, that can predict estuary primary productivity under different scenarios of climate change, sea level rise, sediment loading, and habitat loss. Local actions—fencing stock from riparian edges, afforesting catchments, ending logging on steep slopes—cannot stop the sea from rising, but they can keep the estuary’s lungs working, sustaining the shellfish, fish, biodiversity, and nutrient removal services that depend on them.
Subject of Research: Mapping seasonal and daily dynamics of seafloor primary production in a shallow New Zealand estuary
Article Title: The breathing seascape: Spatial and temporal up-scaling of an estuarine ecosystem function
Article References: Lohrer, A. M., Stephenson, F., Lam-Gordillo, O., MacDonald, I. T., Massuger, J., Paul-Burke, K., Douglas, E. J., Petersen, G. L., & Bulmer, R. H. (2026). The breathing seascape: Spatial and temporal up-scaling of an estuarine ecosystem function. iScience, 29(10), Article 117597. https://doi.org/10.1016/j.isci.2026.117597
Image Credits: AI Generated
DOI: 10.1016/j.isci.2026.117597
Keywords: estuary, primary production, seagrass, benthic ecosystems, aquatic eddy covariance, Ōhiwa Harbour, New Zealand, ocean darkening, ecosystem services, hypoxia, Māori stewardship, coastal management
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Gavin Prescott. (September 25, 2026). Scientists watch a New Zealand estuary breathe, mapping the seafloor’s hidden oxygen pulse. Scienmag. https://scienmag.com/scientists-watch-a-new-zealand-estuary-breathe-mapping-the-seafloors-hidden-oxygen-pulse/
Gavin Prescott. “Scientists watch a New Zealand estuary breathe, mapping the seafloor’s hidden oxygen pulse.” Scienmag, 25 September 2026, https://scienmag.com/scientists-watch-a-new-zealand-estuary-breathe-mapping-the-seafloors-hidden-oxygen-pulse/. Accessed 25 September 2026.
Gavin Prescott. “Scientists watch a New Zealand estuary breathe, mapping the seafloor’s hidden oxygen pulse.” Scienmag. September 25, 2026. https://scienmag.com/scientists-watch-a-new-zealand-estuary-breathe-mapping-the-seafloors-hidden-oxygen-pulse/
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Tags: aquatic eddy covariancebenthic ecosystemscoastal habitat healthcoastal managementecosystem servicesestuarine oxygen dynamicsestuaryEstuary ecosystem monitoringhypoxiainnovative oceanographic techniquesMāori stewardshipmarine ecosystem rhythmsNew ZealandNew Zealand harbor ecologyocean darkeningŌhiwa Harbourprimary productionsatellite limitations in estuariesseafloor primary production mappingseagrassseasonal oxygen flux in estuariesshallow estuary researchunderwater breathing patternsunderwater light absorption challenges
