Within coastal environments, multiple physical processes influence the concentration of nutrients, oxygen, salinity, and other important ecological variables. Many of these physical mechanisms, which include surface and internal waves, tides, winds, and daily heating and cooling, produce considerable nearshore environmental variability on diurnal time scales. In the case of tropical coral reefs, diurnal temperature variability has been previously demonstrated to enhance coral resistance to thermal stress, and therefore reduce the prevalence of bleaching. Here, we ascertain the importance of diurnal temperature variability over other thermal stress metrics for predicting coral bleaching, using a collection of over 100 in situ temperature time series from 5 global reef regions matched with 46 bleaching observations. Results indicate that high-frequency temperature variability is the most influential metric in explaining bleaching outcomes, offering a mitigating effect such that a 1 °C increase in daily temperature range would reduce the odds of more severe bleaching by a factor of 33. Implications for prioritizing reefs for conservation are noted. As there are multiple physical processes driving diurnal temperature variability in the nearshore and within coral reefs, we are further concerned with the role of strong atmosphere-ocean heat fluxes over nonuniform bathymetry, generic features of tropical reef environments, in shaping the nearshore thermal environment. In such regions, surface heat fluxes lead to greater volumetric heating and cooling in shallower waters than adjacent deeper ones, establishing a horizontal temperature gradient that subsequently drives a vertically sheared exchange flow. The importance of this thermally-driven exchange to cross-shore volume and heat transport is apparent in multiple field observations, whereby modulations from alongshore currents are considerable. Using the Regional Ocean Modeling System (ROMS), we investigate the role of steady, upwelling- and downwelling-favorable alongshore currents of varying magnitudes in altering the structure of thermal exchange. Circulation in a base-case simulation with no alongshore forcing demonstrates a robust diurnal pattern consisting of a downslope flow from convective cooling and a buoyant warm front from surface heating, with cross-shore velocities of O(1) cm/s. Mild upwelling- and downwelling-favorable alongshore currents enhance the nearshore temperature gradient, thereby strengthening the thermal exchange. However, as the alongshore current is strengthened, the resulting near-bed shear-generated turbulence induces substantial vertical mixing, dampening temperature gradients and weakening thermally-driven exchange. When the alongshore forcing is further increased such that the associated turbulent mixing homogenizes the water column, the thermally-driven exchange vanishes, yet there remains nontrivial baroclinic cross-shore exchange, which we investigate by invoking bottom Ekman theory. A theoretical model derived from central differences of the classical Ekman balances is used to compute the horizontal velocity profiles resulting from an alongshore bottom stress, and we find that the ability of the theoretical solution to reproduce the expected flow features largely depends on the form of the eddy viscosity. Velocities of the theoretical model are then compared with those of ROMS, which includes nonlinear advection terms in the governing equations. The resulting dynamics and consequences for baroclinic cross-shore exchange of these additional terms are discussed in the context of the alongshore momentum budget.

This thesis investigates the physical processes that govern the transport and environmental history of marine invertebrates during their larval stage, focusing on the role of wind-driven flow and freshwater plumes. Additionally, this work examines how release location and swimming behavior modifies the path and environmental history of a larval particle. The research was conducted by using Regional Ocean Modeling System (ROMS) and a particle-tracking code to estimate the transport of larval-stage invertebrates and their environmental history over the larval duration period (particle paths) in parameters such as temperature, salinity and phytoplankton concentration. Results indicate that swimming particles are retained closer to shore and to their release location compared to passive particles (no swimming behavior). The freshwater plume affects alongshore dispersal of particles released to the south of the Columbia River during downwelling periods and weak upwelling periods, and particles released to the north of the river during downwelling periods. Furthermore, wind-driven circulation can influence the environmental exposure of larval stage marine invertebrates. Particles north of the Columbia River mouth saw greater variation in temperature and salinity, and higher phytoplankton concentration as upwelling index increased. As upwelling intensity increases, southern particles experience lower average temperature, higher salinity, and higher phytoplankton concentration conditions (however, lower phytoplankton concentrations than northern particles). This work suggests that wind-driven circulation and freshwater plumes can play an important role in the distribution and environmental history of larval stage marine invertebrates and this could influence their future persistence along the U.S. West Coast.

Coral reefs worldwide are being threatened by increasing seawater temperatures, ocean acidification, overfishing, pollution, and increased intensity of storms. Small scale spatial (< 1 km) variability in temperature has been observed on coral reefs; however, it currently cannot be measured by remote sensing products. Furthermore, small scale temporal (< 1 cycle/day) variability has been shown to be significant for coral bleaching resilience. Here, I aim to further our understanding of the physical processes which drive the spatial and temporal variability in environmental parameters on reef ecosystems. First, I examine the physical processes driving flow on the east reef flat at Dongsha Atoll, in the northern South China Sea. There are observable thermal microclimates on the shallow and wide reef flat, which distinguishes the reef from open ocean temperatures. A simple analytical model of flow reveals that tides and surface waves are driving flow here, and the influence is variable in time and space. The wide reef flat at Dongsha Atoll leads gradients in the residence time and source of water (offshore vs. lagoon), and an asymmetry in the tidal excursion of water on the reef flat. Next, I investigate the influence of the internal waves on the thermal and nutrient environment on the east reef flat at Dongsha Atoll. A heat budget was created to estimate the temperature on the reef without the internal wave influence, and instantaneous temperatures on the reef can be up to 2.0°C warmer. Also, internal waves increase the instantaneous flux of nutrients onshore by four-fold, which can have significantly influence biogeochemistry on the reef. Finally, high spatial and temporal resolution temperature measurements were collected from three coral reefs with different morphologies, and used to determine the physical processes driving reef scale variability in water temperature. Distinctive thermal environments were observed, including reef-scale gradients in mean temperature and daily temperature range (DTR), which distinguish the shallow reefs from offshore. Daily temperature range has been shown to be the most influential metric in predicting bleaching prevalence on reefs, and studies have shown it can be predicted from average water depth. By using a heat budget, and including advection in the estimate of temperature, we are able improve predictions of DTR with minimal in-situ measurements.

Oxygen levels in the global coastal ocean have drastically decreased in past decades with a surge in reported hypoxic events. In most coastal systems, hypoxia is induced through eutrophication, long residence times, and lack of ventilation to the atmosphere. Understanding the complex physical and biogeochemical processes in these systems is crucial for ecosystem health and resilience.

Dongsha Atoll is a coral atoll and Taiwanese National Park located in the northern South China Sea. In summers 2014 and 2015, hypoxia-related fish kills, coral bleaching, and sea grass die offs were observed on the eastern edge of Dongsha Atoll lagoon, motivating further work to understand the key drivers of hypoxia. This body of work focuses on a field campaign in summer 2019. Here, I aim to further our understanding of how physical-biogeochemical interactions drive oxygen availability in tropical reef-lagoon systems.

First, I construct a heat and volume budget for the lagoon to understand the physical processes governing heating, circulation, and ocean-lagoon exchange. Results show that surface heat fluxes drive rapid heating of the lagoon by ~1.5°C over the 22-day study period. Advective transport over the reef flat from tide- and wave-driven flows is an important component of ocean-lagoon exchange that is balanced by a net outflow through the channels on subtidal timescales. Specifically, a near phase-locked interaction between diurnal solar forcing and near-diurnal tidal exchange drives persistent advective cooling over the reef flat.

Next, in order to understand the physical processes governing residence time and renewal of the bottom waters, I construct a bottom water mass budget in Dongsha Atoll lagoon. Results show frequent bottom water renewal events driven by tidally modulated advective processes through the lagoon channels and over the reef flat. Though bottom water renewal events are usually a mechanism for refreshing oxygen levels in stratified systems, the water advected into Dongsha Atoll lagoon from the reef flat can, at times, be hypoxic. The water flowing off of the reef flat into the Dongsha Atoll lagoon is intermittently oxygen deficient, due to seasonal phase-alignments between the primarily diurnal tidal flow and biological respiration on the reef. During the study period, the flood phase of the tide, which drives flow of cooler offshore water across the reef flat from the ocean to the lagoon, occurred at night when strong biological respiration draws down oxygen on the shallow reef flat. These cooler, low oxygen waters sink to the bottom of the stratified lagoon waters, creating a pool of isolated low-oxygen water.

Lastly, I examine the drivers of low oxygen on the east reef flat of Dongsha Atoll. Results show that the diurnal biological cycle on the reef flat is in phase with diurnal flood-at-night tidal forcing, which together leads to strong nocturnal oxygen drawdown. Lagoonward flow at night then transports the low oxygen water to the lagoon boundary. This process results in episodic low-oxygen events at depth inside the lagoon. We show that this pattern is seasonal on Dongsha Atoll due to the annual phasing of the diurnal tides, with the flood phase of the tide consistently occurring at night during summer months. Our findings underscore the potential significance of physical-biological interactions in other reef systems with diurnal tides, emphasizing the need for further work to elucidate oxygen dynamics in coastal tropics.