A seasonal study of phytoplankton and zooplankton was conducted from 1999 to 2001 in Pensacola Bay, Florida, USA, to further the understanding of pelagic food webs in sub-tropical estuaries. Monthly measurements included size-fractionated chlorophyll (whole water, <5 μm, <20 μm), net- and picophytoplankton composition analyzed using microscopy, flow cytometry, and HPLC pigment analysis. Additionally, zooplankton abundance and dry weight were determined from net tows. The results show a phytoplankton community dominated by the small size fraction (<5 μm), especially during the warm periods. The 5–10 μm) were predominantly composed of diatoms, followed by chlorophytes, cryptophytes and dinoflagellates. The three most abundant genera of diatoms were Thalassiosira, Pennales and Cyclotella. Zooplankton biomass averaged 12.2 μg C L⁻¹, with peak biomass occurring during May (∼30 μg C L⁻¹). Zooplankton abundance averaged 16.7 ind. L⁻¹, peaking at 30 ind. L⁻¹ during May. During the summer, the zooplankton community shifted from the ubiquitous Acartia tonsa towards Oithona sp. The increase in Oithona coincided with increases in picophytoplankton and may reflect the changing food resources available to zooplankton. Thus, the trophic implications of cyanobacterial dominance in sub-tropical estuaries need to be more fully assessed.

Dissolved inorganic carbon (DIC), total alkalinity (TAlk), pH, and dissolved oxygen (DO) were determined in the Mississippi River plume during five cruises conducted in the spring, summer, and fall. In contrast to many other large rivers, both DIC and TAlk were higher in river water than in seawater. Substantial losses of DIC, relative to TAlk, occurred within the plume, particularly at intermediate salinities. DIC removal was accompanied by high DO, high pH, and nutrient depletion, and was attributed to high phytoplankton production. As a result, the carbonate saturation in the plume became much higher than in ocean and river waters. A mixing model was used to determine DIC removal. We provide evidence that the use of a two—end‐member (river and ocean) mixing model was valid during late summer and fall (low discharge period). However, for other periods we used salinity and TAlk to delineate a mixing model that included two river end members and an ocean end member. Net community production rates in the plume, estimated using a box model, peaked in the summer and were among the highest reported to date for large river plumes. In the summer and fall, biological production in the river plume consumed a majority of the available nutrients, whereas during the spring only a small fraction of the available nutrients were consumed in the plume. Biological production was the dominant process influencing pH and carbonate saturation state along the river—ocean gradient, whereas physicochemical dynamics of mixing played an important role in controlling the TAlk and DIC distributions of this large river plume.

River‐dominated continental shelf environments are active sites of air‐sea CO₂ exchange. We conducted 13 cruises in the northern Gulf of Mexico, a region strongly influenced by fresh water and nutrients delivered from the Mississippi and Atchafalaya River system. The sea surface partial pressure of carbon dioxide (pCO₂) was measured, and the air‐sea CO₂ flux was calculated. Results show that CO₂ exchange exhibited a distinct seasonality: the study area was a net sink of atmospheric CO₂ during spring and early summer, and it was neutral or a weak source of CO₂ to the atmosphere during midsummer, fall, and winter. Along the salinity gradient, across the shelf, the sea surface shifted from a source of CO₂ in low‐salinity zones (0≤S<17) to a strong CO₂ sink in the middle‐to‐high‐salinity zones (17≤S<33), and finally was a near‐neutral state in the high‐salinity areas (33≤S<35) and in the open gulf (S≥35). High pCO₂ values were only observed in narrow regions near freshwater sources, and the distribution of undersaturated pCO₂ generally reflected the influence of freshwater inputs along the shelf. Systematic analyses of pCO₂ variation demonstrated the importance of riverine nitrogen export; that is, riverine nitrogen‐enhanced biological removal, along with mixing processes, dominated pCO₂ variation along the salinity gradient. In addition, extreme or unusual weather events were observed to alter the alongshore pCO₂ distribution and to affect regional air‐sea CO₂ flux estimates. Overall, the study region acted as a net CO₂ sink of 0.96 ± 3.7 mol m⁻² yr⁻¹ (1.15 ± 4.4 Tg C yr⁻¹).