Papers reporting the results of dynamic simulation models of aquatic ecosystems tend to show predicted concentrations of the state variables. The phytoplankton compartment is typically represented as predicted biomass, expressed as the concentration of chlorophyll a, particulate carbon, or particulate nitrogen. While computed values of phytoplankton biomass generally agree with observations, many of these same models significantly underestimate primary production. Existing simulation models often base the calculation of primary production on the Eppley curve, which sets the maximum daily phytoplankton growth rate as a function of temperature. Despite the apparent wide applicability of the Eppley curve, an increasing number of culture and field studies have measured growth rates in excess of those predicted by the curve, which may explain why existing models often underestimate primary production. An alternate empirical formulation which predicts daily phytoplankton production from biomass, photic depth, and incident irradiance has been shown to apply in a variety of nutrient-rich estuarine systems. Despite the large number of systems in which these empirical models have been developed, they predict remarkably similar rates of daily and annual production. Furthermore, these empirical models predict rates of production in excess of those predicted by the Eppley curve. The empirical formulation therefore presents an alternative to the Eppley curve in dynamic ecosystem models, and may result in more accurate predictions of primary production by these models.

Declines in the seagrass Zostera marina L. in estuaries and lagoons have been attributed in part to reductions in irradiance reaching the seagrass blades. Epiphytes growing on Z. marina have the potential to attenuate a large fraction of the light that would otherwise reach the blades. This problem has previously been studied by measuring light penetration through homogenized epiphytic slurries or through glass slides fouled with epiphytes. However, the latter may not represent the natural succession or species composition found on live Z. marina leaves and the former does not preserve the structure of the epiphytic complex. Further, past studies have not measured attenuation across the full range of epiphytic densities found in the field. In this study, we measured light penetration across a wide range of epiphytic densities by holding scraped and unscraped Z. marina blades over a submerged light sensor. Results compared well with past studies at low epiphyte densities, with strong reductions in light penetration as density increased. However, at higher densities, penetration leveled off to a relatively constant value as the epiphytes floated out from the edges of the blade. Studies using slurries did not capture this phenomenon and thus predicted decreasing penetration down to 0%.

A comprehensive carbon budget was constructed to quantify carbon flows through the freshwater‐marine continuum of a temperate, microtidal estuary. We performed coordinated measurements of dissolved inorganic carbon and total organic carbon fluxes to resolve spatial variability between and along the channel and shoals and diel variability across the entire estuary for 2 yr. Net ecosystem metabolism (NEM) was the most significant control on carbon flow within estuary regions. However, metabolic rates were spatially coupled such that counteracting fluxes across the channel‐shoal gradient or along the river‐ocean gradient resulted in system‐wide NEM that was closely in balance (–3.0 ± 3.3 to 1.1 ± 4.4 molC m−2 yr−1). Similarly, large diel and seasonal variability in air–water CO2 fluxes were observed during 72 spatial surveys, but these short‐term variations generally cancelled out when aggregated to annual budget terms. Although atmospheric exchanges were small (–0.2 ± 0.1 to 2.0 ± 0.4 molC m−2 yr−1), they were subject to large errors (± 4 molC m−2 yr−1) if diel variability was neglected. Internal mechanisms that maintained balanced carbon flows were strongly impacted by river discharge and were only apparent by separately quantifying channel and shoal fluxes. Notably, metabolic responses of the shoal to river forcing outweighed the responses of the channel, and the net impact was contrary to prior relationships derived from synthesis of lower‐resolution carbon budgets. Our budget demonstrates that resolution of carbon fluxes at appropriate scales, including channel‐shoal and diel variability, is critical to characterizing ecosystem function and the fate of carbon within the river‐ocean continuum.

Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear, because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.

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