EXECUTIVE SUMMARYCoastal environments are an important component of the global carbon cycle, and probably more vulnerable than the open ocean to anthropogenic forcings. Due to strong spatial heterogeneity and temporal variability, carbon flows in coastal environments are poorly constrained. Hence, an integrated, international, and interdisciplinary program of ship-based hydrography, Voluntary Observing Ship (VOS) lines, time-series moorings, floats, gliders, and autonomous surface vessels with sensors for pCO 2 and ancillary variables are recommended to better understand present day carbon cycle dynamics, quantify air-sea CO 2 fluxes, and determine future long-term trends of CO 2 in response to global change forcings (changes in river inputs, in the hydrological cycle, in circulation, sea-ice retreat, expanding oxygen minimum zones, ocean acidification, …) in the coastal oceans. Integration at the international level is also required for data archiving, management, and synthesis that will require multi-scale approaches including the development of biogeochemical models and use of remotely sensed parameters. The total cost of these observational efforts is estimated at about 50 million US dollars per year.

Tropical urban estuaries are severely understudied. Little is known about the basic biogeochemical cycles and dominant ecosystem processes in these waterbodies, which are often low lying and heavily modified. The San Juan Bay Estuary (SJBE) in San Juan, Puerto Rico, is an example of such a system. Over the past 80 years, a portion of the estuary has filled in, changing the hydrodynamics and negatively affecting water quality. Here we sought to document these changes using ecological and biogeochemical measurements of surface sediments and bivalves. Measurements of sediment physical characteristics, organic matter content, and stable isotope ratios (δ13C, δ15N, δ34S) illustrated the effects of the closure of the Caño Martín Peña (CMP) on the hydrology and water quality of the enclosed and semi‐enclosed parts of the estuary. The nitrogen stable isotope (δ15N) values were lowest in the CMP, the stretch of the SJBE that is characterized by waters with low dissolved oxygen and high fecal coliform concentrations. Despite this, the results of this study indicate that nitrogen (N) contributions from N‐fixing, sulfate‐reducing microbes may meet or even exceed contributions from urban runoff and sewage. While the importance of sulfate reducers in contributing N to mangrove ecosystems is well documented, this is the first indication that such processes could be dominant in an intensely urban system. It also underscores just how little we know about tropical coastal ecosystems in densely populated areas throughout the globe.

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Mangroves sequester significant quantities of organic carbon (C) because of high rates of burial in the soil and storage in biomass. We estimated mangrove forest C storage and accumulation rates in aboveground and belowground components among five sites along an urbanization gradient in the San Juan Bay Estuary, Puerto Rico. Sites included the highly urbanized and clogged Caño Martin Peña in the western half of the estuary, a series of lagoons in the center of the estuary, and a tropical forest reserve (Piñones) in the easternmost part. Radiometrically dated cores were used to determine sediment accretion and soil C storage and burial rates. Measurements of tree dendrometers coupled with allometric equations were used to estimate aboveground biomass. Estuary-wide mangrove forest C storage and accumulation rates were estimated using interpolation methods and coastal vegetation cover data. In recent decades (1970–2016), the highly urbanized Martin Peña East (MPE) site with low flushing had the highest C storage and burial rates among sites. The MPE soil carbon burial rate was over twice as great as global estimates. Mangrove forest C burial rates in recent decades were significantly greater than historic decades (1930–1970) at Caño Martin Peña and Piñones. Although MPE and Piñones had similarly low flushing, the landscape settings (clogged canal vs forest reserve) and urbanization (high vs low) were different. Apparently, not only urbanization, but site-specific flushing patterns, landscape setting, and soil fertility affected soil C storage and burial rates. There was no difference in C burial rates between historic and recent decades at the San José and La Torrecilla lagoons. Mangrove forests had soil C burial rates ranging from 88 g m–2 y–1 at the San José lagoon to 469 g m–2 y–1 at the MPE in recent decades. Watershed anthropogenic CO2 emissions (1.56 million Mg C y–1) far exceeded the annual mangrove forest C storage rates (aboveground biomass plus soils: 17,713 Mg C y–1). A combination of maintaining healthy mangrove forests and reducing anthropogenic emissions might be necessary to mitigate greenhouse gas emissions in urban, tropical areas.