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.
The dissolved oxygen (DO) concentration in the bottom waters of western Long Island Sound decreases to hypoxic levels between April and July. Since the rate of decline of DO is considerably less than measured respiration, there must be significant vertical transport of DO from oxygen richer waters near the surface and/or horizontal transport from the central Sound. Simple model budgets with either of these sources are able to provide predictions of the seasonal rate of decline that are consistent with the observed values. Although prior budget estimates indicated that vertical fluxes were a significant portion of the resupply of DO, these were not able to discount the possible importance of horizontal fluxes, nor have there been any measurements of horizontal fluxes in this region. We present an analysis of time series of moored conductivity, temperature, DO, and current observations in the hypoxic area of Long Island Sound during the summers of 2005 and 2006. We estimate the near-bottom along-channel flux divergences of salt, heat, and DO as 0.11 6 0.08 g kg 21 d 21 , 25 6 6 W m 23 , and 4 6 6 lM d 21 , respectively. Since this horizontal DO transport is only 25% of the magnitude of the mean rate of respiration, we conclude that vertical transport by mixing forms the bulk of the physical resupply of DO to the hypoxic zone of the western Sound.
In estuaries, tidal period variations in the rate of vertical mixing have been observed to result from various causes: in Liverpool Bay and the York River, they have been attributed to tidal straining of the along‐channel density gradient modulating stratification; in the Hudson River they arise from tidal modulation of the height of the tidal current bottom boundary layer (BBL). Along continental shelves, tidal period fluctuations in mixing have been observed to result from the dissipation of internal waves (IWs). Western Long Island Sound (WLIS) moored instrument records indicate that large near‐bottom increases in dissolved oxygen (DO) and heat and a decrease in salt occur during the middle of the flood tide: an analysis of water mass signatures indicates that the transport involved is vertical and not horizontal. Temperature data from a vertical thermistor array deployed in the WLIS for 16 days in August 2009 clearly show a tidal cycle of IW activity creating a mean thermocline depression at midflood of approximately 25% of the water depth with individual IW thermocline depressions of as much as 50% of the water depth. Contemporaneous ADCP measurements show increases in shear due to IWs during the flood. Near‐bottom internal wave activity is maximal at and after midflood and is correlated with near‐bottom temperature and DO tendencies at both tidal and subtidal scales. We conclude that internal tides are an important vertical mixing mechanism in the WLIS through both increased shear from IWs and displacement of the pycnocline into the region of high shear in the BBL.
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