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Integrating spatial heterogeneity into assessments of salt marsh biogeochemistry is becoming increasingly important because disturbances that reduce plant productivity and soil drainage may contribute to an expansion of shallow ponds. These permanently inundated and sometimes prominent landscape features can exist for decades, yet little is known about pond biogeochemistry or their role in marsh ecosystem functioning. We characterized three ponds in a temperate salt marsh (MA, USA) over alternating periods of tidal isolation and flushing, during summer and fall, by evaluating the composition of plant communities and organic matter pools and measuring surface water oxygen, temperature, and conductivity. The ponds were located in the high marsh and had similar depths, temperatures, and salinities. Despite this, they had different levels of suspended particulate, dissolved, and sediment organic matter and abundances of phytoplankton, macroalgae, and Ruppia maritima. Differences in plant communities were reflected in pond metabolism rates, which ranged from autotrophic to heterotrophic. Integrating ponds into landcover‐based estimates of marsh metabolism resulted in slower rates of net production (−8.1 ± 0.3 to −15.7 ± 0.9%) and respiration (−2.9 ± 0.5 to −10.0 ± 0.4%), compared to rates based on emergent grasses alone. Seasonality had a greater effect on pond water chemistry, organic matter pools, and algal abundances than tidal connectivity. Alternating stretches of tidal isolation and flushing did not affect pond salinities or algal communities, suggesting that exchange between ponds and nearby creeks was limited. Overall, we found that ponds are heterogeneous habitats and future expansion could reduce landscape connectivity and the ability of marshes to capture and store carbon.

We studied marsh-atmosphere exchange of carbon dioxide in a high marsh dominated salt marsh during the months of May to October in 2012-2014. Tidal inundation at the site occurred only during biweekly spring tides, during which we observed a reduction in fluxes during day and night. We estimated net ecosystem exchange (NEE), gross primary production (GPP), and ecosystem respiration (R eco ) using a modified PLIRTLE model, which requires photosynthetically active radiation, temperature, and normalized difference vegetation index (NDVI) as control variables. NDVI decreased during inundation, when the marsh canopy was submerged. Two-time series of NDVI, including and excluding effects of tidal inundation, allowed us to quantify the flux reduction during inundation. The effect of the flux reduction was small (2-4%) at our site, but is likely higher for marshes at a lower elevation. From May to October, GPP averaged −863 g C m −2 , R eco averaged 591 g C m −2 , and NEE averaged −291 g C m −2 . In 2012, which was an exceptionally warm year, we observed an early start of net carbon uptake but higher respiration than in 2013 and 2014 due to higher-air temperature in August. This resulted in the lowest NEE during the study period (−255.9 ± 6.9 g C m −2 ). The highest seasonal net uptake (−336.5 ± 6.3 g C m −2 ) was observed in 2013, which was linked to higher rainfall and temperature in July. Mean sea level was very similar during all 3 years which allowed us to isolate the importance of climatic factors.

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