Three-dimensional modeling of wave-driven physical and biogeochemical processes in lakes and coral reefs

Spatially and temporally explicit numerical models were developed to investigate two distinct wave-driven systems. Firstly the generation of internal waves in a deep-water lake system and secondly, the combined effect of hydrodynamic and biogeochemical processes on the distribution of nutrients, benthic nutrient fluxes and alkalinities across a shallow-water fringing coral reef system. Accurately predicting the response of these variables and processes to external forcing and its resulting fine-scale spatial variability was imperative in both studies. In the well-stratified lake system, fetch-dependent wave spectra induced spatial variability in the surface roughness and, therefore, the surface drag coefficients. Spatially varying wave and wind fields were interpolated from the measurements from several locations across the lake and used to force a three-dimensional numerical hydrodynamic model (ELCOM). There was a statistically significant impact of this spatial variability on the local generation of highfrequency internal waves, but not on the low-frequency principal modes, which were determined by the spatial-mean wind impulse. In the coastal fringing reef system, incident ocean swell surface waves were found to be the main driver of nearshore reeflagoon circulation as well as mass transfer of nutrients to benthic reef communities. To model the uptake of nutrients, we developed a new benthic biogeochemical module using relationships from the coral reef literature relating convective nutrient mass transfer velocities to total bottom drag and integrated it in a coupled three-dimensional numerical ocean circulation model (ROMS) and numerical spectral wave model (SWAN). The coupled model showed high spatial variation in nutrient concentration and successfully reproduced the nutrient concentration across a section of Ningaloo Reef at Sandy Bay. The coupled physical-biogeochemical model was further extended to investigate the system-scale response to reef