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Due to their high biological productivity, continental shelf seas are significant sinks of anthropogenic carbon. To better understand the cycling of carbon within them, an accurate prediction of their vertical density stratification is required, as this is a critical control on the carbon drawdown. While the dominant controls on density structure are boundary driven mixing and seasonal heating, internal waves have been shown to play a small but critical role in both open ocean and shelf sea physical and biogeochemical cycles. Current knowledge on the spatial and temporal variability in internal mixing is however still severely limited. The aim of the work in this thesis was to develop new insight into the seasonal variability of physical controls on the vertical density structure and examine its biogeochemical responses in a temperate shelf sea. This thesis presents and examines new results that test the impact of boundary layer and internal wave forcing on stratification and vertical density structure in continental shelves. A new series of continuous measurements of full depth density and velocity structure, meteorological and wave forcing, surface nitrate and surface chlorophyll a spanning 17 months (March’14 − July’15) provide unprecedented coverage over a full seasonal cycle at a station 120 km north-east from the continental shelf break. Work within this thesis showed that the controls on vertical density structure at the mooring site were largely analogous to that of open-ocean environments with tidal mixing only playing a minor role. This result contrasts with the well-known tidally controlled frontal systems described by Simpson and Hunter (1974). Since a large proportion of continental shelf regions are away from tidal mixing fronts this result suggest the requirement for an adjusted third regime that bridges the gap between open-ocean environments and frontal regions, to accurately predict the vertical density structure within them. The long-term observations presented in this thesis reveal a seasonality within the internal wave energy, which suggest internal mixing varying relative to the seasonal cycle of stratification, represented by N2. By investigating the representation of this seasonality by three commonly used internal wave parameterisations it was shown that each predicted a seasonality that directly contradicted that observed within the internal wave energy. It was suggested that the reason for this was most likely due to their failure to introduce the enhanced S2 that is attributable to internal waves, which have been shown in this work to have a strong seasonal cycle with maximum energy levels during the summer. In an attempt to provide realistic scaling of turbulence an adjusted iteration of the MacKinnon and Gregg (2003a) scaling of turbulence was employed using an observed close relationship between N2 and S2 to introduce a state of marginal stability in the pycnocline, thus introducing a seasonally varying level of internal mixing that follows the observed seasonality in internal wave energy. Examining the biogeochemical response to the seasonal change in vertical density struc- ture also highlighted the importance of the autumn phytoplankton bloom within the annual cycle of primary production. By putting the autumn phytoplankton bloom within the context of the seasonal cycle it was shown that it has the potential to be as productive as the well-studied spring phytoplankton bloom and the summer sub-surface chlorophyll maximum and thus has the capacity to significantly contribute to the drawdown of atmospheric carbon dioxide.

The world ocean can broadly be split into two regimes, the shallow shelf seas up to a few hundred metres deep and the deep open ocean which is typically 4-5 km deep. These two regimes are separated by a narrow region of steep topography. This steep topography acts to limit the exchange to those processes that break the assumptions of geostrophy. This exchange, however, is important on both a local and global scale. The shelf seas are an important source of dense water masses, ventilating the deep ocean, control of the flux of mid-depth open ocean heat to glacial fronts, supply of nutrients from the open ocean to sustain enhanced productivity on the shelf, and export of the carbon drawn-down by this productivity into the deep ocean. This problem will be explored through two themes, one exploring the role of the bolus transport and one exploring an integral framework. The bolus transport is de ned as the transport as a result of co-variances in layer thickness and layer velocity. This has previously been extensively applied for the atmosphere and the action of eddies in the Southern Ocean. Here the bolus transport driven by the action of the internal tide near the shelf edge is considered. First we consider a sinusoidal internal wave on the interface of a two well mixed layer ocean. This leads to a theoretical scaling for the bolus transport of (ca2)=(2hi) in the same direction as the propagation of the wave. The bolus transport was then calculated for eight moorings across four locations. For the surface layer these transports were in the range 1.09 to 0.1 m2s 1 and for the bottom layer were in the range 1.06 to 0.04 m2s 1. These observational estimates compare favourably with the estimates from the theory, with the theory within 40% of the observed values. This bolus transport is balanced locally by a time-mean velocity of equal magnitude but directed off shelf in both layers. The Walin Framework is an integral framework describing the rate at which water crosses density surfaces. This is used to diagnose the formation, or destruction, rate of water within density classes across the European Shelf, bounded by the 200m isobath, the southern limit of the Celtic Sea and the Norwegian Coast. This formation rate makes the largest contribution to the exchange across the shelf edge. This reveals three distinct regimes: an off-shelf transport in the lightest classes of 0.5 Sv, an on-shelf transport in the middle density classes of 1.5 Sv, and an off shelf transport in the densest classes of 1 Sv. Mapping these along the shelf edge indicates that much of the shelf does not reach the lightest classes so only the intermediate and dense regime is applicable. The lightest regime primarily exists along the southern section of the Norwegian Trench. This implies two circulations: a down-welling circulation of 1 Sv across much of the European Shelf and an across shelf transport of 0.5 Sv, on-shelf across much of the shelf edge balanced by an off shelf transport in the Norwegian Trench. This down-welling circulation is similar to previous estimates of the total transport across the European Shelf Break.