Small, shallow, low-inflow estuaries (LIEs) are common worldwide along steep coasts in regions with low or seasonal precipitation. LIEs along coasts with strong wave conditions are termed bar-built estuaries (BBEs) where a sand-bar sill near the mouth due to current and wave-driven sediment transport. The sill height and location can have profound impacts on the circulation, inundation, stratification, and dissolved oxygen in the estuary. In intermittently closed estuaries (ICEs) the sill can periodically accrete to block the ocean-estuary exchange. In Los Peñasquitos Lagoon, an ICE in Southern California, the hydrodynamic variability of these traditionally under-researched systems is investigated through extensive observations.

Four and half years of continuous hydrodynamic observations over several periods of climatology add valuable insight into how ICEs respond to changing nearshore and upstream forcings. Observations during the open state reveal that when the sill near the mouth is low, the estuary functions like a canonical estuary with evidence of strain-induced period stratification and canonical exchange flows. As the sill accretes, tidal circulation weakens, and the estuarine exchange does not scale with the canonical pressure-friction balance.

When the inlet closes, estuary-ocean exchange is interrupted, and estuarine water levels increase due to freshwater inflows and overtopping. Reduced mixing due to interrupted tidal exchange and increased stratification due to freshwater inputs lead to hypoxic conditions developing at depth. The diurnal circulation when closed is forced by differential heating and cooling driving thermal exchange that can be weakened by strong diurnal winds.

To put the dynamics of LPL in context with similar estuaries, water levels were measured in 12 additional Southern California estuaries during the 2015-2016 El Niño winter. Water levels inside perennially open estuaries mirrored ocean water levels. ICEs exhibited enhanced higher-high water levels than offshore during large waves, and lower-low water levels were truncated due to the sill at the mouth, resulting in elevated detided water levels. The sill height and wave exposure were important to the individual estuarine response to ocean conditions. Understanding how LIEs, BBEs, and ICEs respond to increased sea levels and waves and the factors that influence closures will help managers develop appropriate adaptation strategies.

Infragravity (IG) waves (periods ~ 25 s to 250 s) are known to dominate wave energy inside many shallow, bar built estuaries. However, beyond their importance for sediment buildup at the sill, little is known about the impact of IG waves on these shallow estuaries. I use observations from a focused deployment in Los Peñasquitos Lagoon in Southern California during a period of large wave forcing to understand the impacts of IG waves, with a particular focus on the turbulence generated through bottom friction. I also reflect on increasing pressure for scientists to work closely with lagoon managers in the development of their questions and conduct a study of academic culture to understand how similar changes are affecting coastal physical oceanographers. In Chapter 2, I describe the field deployment in detail and use initial observations to link IG waves to sediment transport and oscillations of salinity and temperature in the estuary. In Chapter 3, I develop new methods for despiking Accoustic Doppler Velocimeter (ADV) data and calculating turbulent dissipation from velocity measurements in the presence of IG waves. In particular I develop a new inertial subrange fitting method to improve turbulent dissipation measurement accuracy in any measurement conditions. In Chapter 4, I use those dissipation measurements to develop a new method for predicting turbulent dissipation in the wave boundary layer. I verify this method with a numerical model and observations, and use it to show that IG waves significantly increase turbulence in the estuary during neap tides and at the beginning of flood tide. In Chapter 5, I conduct 15 interviews of coastal physical oceanography professors in the United States. Using these interviews, I show that a disconnect between a relatively slowly changing academic culture and relatively swiftly changing external pressures have led to increased stress and a general over commitment of time for especially new professors in the field.

Oceanic uptake of atmospheric heat as well as incorporation of freshwater occurs across a vast range of spatial scales. Subsequently, these buoyant water masses are transported and modified within the ocean interior. Several physical processes relevant to the transport and mixing of heat and freshwater at an array of coastal scales, ranging from 1000s of km at the continental shelf slope to m within estuaries, are the topic of this dissertation. Analysis of a mix of data assimilative and idealized numerical models and field observations has yielded several impactful results that have direct relevance to coastal societies and ecosystems. At the largest scale, a mechanism that delivers warm water within the Antarctic Circumpolar Current to the continental shelf slope where it crosses into the Amundsen Sea outer shelf has been identified. Vorticity input by wind-stress curl results in the poleward motion of heat that has potential to contribute to Antarctic Ice Sheet mass loss and consequently, global sea level rise. At the much smaller scales of the inner-shelf to surf zone, surface gravity wave induced onshore currents and mixing drastically modify low inflow estuarine freshwater outflows by reducing offshore transport and elongating alongshore and vertical extent within the surf zone. Because the freshwater distribution can be thought of as a proxy for tracers such as pollution, nutrients, or other plume constituents, these results have strong implications for beach contamination among other concerns that frequently arise due to the presence of buoyant outflows in the nearshore region. Within the estuary, lateral circulation moves channelized waters to regions of enhanced productivity over bathymetric shoals. In San Diego Bay, a low inflow estuary that lies in a unique parameter space among estuaries, this process is, at least in part, due to differential advection. Field data suggest that this process is sensitive to seasonal variation in buoyancy inputs and that circulation patterns may be altered in future climate change scenarios, thus impacting the wildlife that utilize the bay for breeding, habitat, and foraging. As such, the findings of this dissertation advance the fundamental science necessary to contribute to many societally relevant coastal management issues.

The topography of an environment is critical for influencing the hydrodynamics of a region and allowing diverse ecosystems to exist in areas with, otherwise, low productivity. We investigate the flow response associated with interactions of large-scale waves with bathymetry of two distinct spatial scales: coral reefs (O(1 km)) and seamounts (O(100 km)).

Momentum balances over coral reefs have mostly been estimated for cross-reef flow in wavy environments. In contrast, we examine the effect of coral reef roughness on alongshore tidal momentum; this is accomplished using month-long pressure, temperature, and velocity observations gathered over a 2-km stretch of a Hawaiian fringing reef system. We find that temporal acceleration plays an important role in the momentum balance. The two dominant forces affecting the alongshore depth-averaged flow acceleration are the tidal pressure gradient and the drag exerted by the coral reef bottom. We estimate drag coefficients and discuss the importance of coral reef drag throughout a tidal cycle.

The interaction between flow and bathymetry on a larger scale is studied using, primarily, satellite data and numerical model output in tropical regions of the Indian Ocean. Satellite observations are employed to characterize the generation of quasi-biweekly Yanai waves, oscillations with a wavelength estimated around 4,000 km, roughly 63% of the width of the equatorial Indian Ocean. These observations provide the first full picture of a quasi-biweekly Yanai wave in the Indian Ocean. Careful analysis suggests that these waves are generated in the western region of the basin, near the Seychelles Plateau, a relatively shallow (60-100m), large (~200 km), steep submarine platform. We examine the connection between Yanai waves and the Seychelles Plateau using model output from the global Los Alamos Parallel Ocean Program Model 2 (POP2), a theoretical stratified seamount-trapped wave model, and limited mooring data. POP2 output suggests that Yanai wave energy enters the Plateau system near the surface, at the western edge, inducing a resonant trapped wave response. The trapped wave redistributes equatorial energy to smaller scales, vertically in the water column, and anticyclonically along the Plateau circumference.