A carbon cycle model is built to describe the behavior of carbon materials in the Pearl River Estuary (PRE), China. The distributions and transformations of dissolved inorganic carbon (DIC), dissolved organic carbon (DOC), and particulate organic carbon (POC) are simulated in the water column and sediment for the year 2006. The terrestrial carbon input is the dominant factor that determines the seasonal variation of carbon, while physical and biochemical processes contribute to the spatial‐temporal circulation of carbon. The simulation results reveal that the PRE acts as a net source for atmospheric CO2 throughout the year, and it buffers the export of DIC from the river and sediment to the adjacent system via the DIC consumption by primary production. As a consequence of biochemical processes, the PRE exports more organic carbon to the sediment and adjacent marine ecosystems than the amount that it receives from upstream river reaches. POC burial in sediment and refractory DOC export to the adjacent marine ecosystems are the main carbon fixation pathways in the PRE. The total amount of carbon fixation in PRE is estimated 6.92 × 1010 mol C year−1. Carbon fixation analysis shows that (1) 20.4% of the POC deposited into sediment is fixed through burial, while the remaining continues to participate in the circulation of carbon materials, and (2) the combined effects of river discharge and monsoon dominate the amount and direction of refractory DOC exports.

A validated hydrodynamic-biogeochemical model was applied to investigate the effects of physical forcing (i.e., river discharge, winds, and tides) on the summertime dissolved oxygen (DO) dynamics and hypoxia (DO < 3 mg L−1) in the Pearl River estuary (PRE), based on a suite of model sensitivity experiments. Compared with the base model run in 2006 (a wet year), the simulated hypoxic area in the moderate year (with 75% of river discharge of the base run) and the dry year scenario (with 50% of river discharge of the base run) was reduced by ~30% and ~60%, respectively. This is because under the lower river discharge levels, less particulate organic matter was delivered to the estuary that subsequently alleviated the oxygen demand at the water–sediment interface, and in the meantime, the water stratification strength was decreased, which facilitated the vertical diffusion of DO. Regarding the effect of winds, the highly varying and intermittent strong winds had a significant impact on the replenishment of bottom DO by disrupting water stratification and thus inhibiting the development of hypoxia. Sensitivity experiments showed that the hypoxic area and volume were both remarkably increased in the low wind scenario (with a bottom hypoxic zone extending from the Modaomen sub-estuary to the western shoal in Lingdingyang Bay), whereas hypoxia was almost absent in the strong wind scenario. The DO budget indicated that winds altered the bottom DO mostly by affecting the DO flux due to vertical diffusion and horizontal advection, and had a limited influence on the DO consumption processes. Moreover, the DO concentration exhibited remarkable fluctuations over the spring-neap tidal cycles due to the significant differences in vertical diffusion. The results of a tide-sensitivity experiment indicated that without tide forcing, most of the shallow areas (average water depth < 5 m) in the PRE experienced severe and persistent hypoxia. The tides mainly enhanced mixing in the shallow areas, which led to higher vertical diffusion and enhanced replenishment of bottom DO.

The selectivity of Perinereis aibuhitensis larvae on different sediment types was studied using an experimental behavioral device in the lab. There were six types of sediment with different organic matter content: 2.19, 2.30, 2.86, 3.25, 3.51, and 5.52%. The results indicated significant differences in the six treatments’ organic matter content (p &lt; 0.05). When the P. aibuhitensis larvae initially attached to the sediment, the larvae’s density showed no significant difference among the six treatments. The density of larvae decreased gradually during the experimental period. It increased with the increasing organic matter content in sediment at every sampling time, but there was no significant difference (p &gt; 0.05). The larvae’s specific growth rate in the first month was significantly higher than those in the second and third months (p &lt; 0.05). The mortality showed no significance at different sediments in equal sampling times, but the mortality was lower in high organic matter content sediments. This study showed that the P. aibuhitensis larvae did not make an active selection; random selection happened when initially attached to the sediment with different organic matter contents. Higher organic matter content in the sediment was more conducive to larvae survival, and the organic matter content is the limitation factor on the mortality and the density. The different densities in the natural habitat of P. aibuhitensis might occur due to the passive selection by the environment.

In coastal areas, organic matter oxidation and the decreased buffering capacity further aggravate acidification in the subsurface by another ∼0.34 pH (Cai et al., 2011). With combined climatic and anthropogenic influences, coastal ecosystems are facing more severe and complex OA that may be intensified in the future (Cai et al., 2011).The estuary receives a large amount of freshwater discharge, terrestrial nutrients and organic materials from upstream (Doney, 2010;Levin et al., 2015;Rabouille et al., 2001), which results in a more active biochemical reaction system in coastal areas. The strong terrestrial nutrients influx can cause eutrophication in estuaries (