The first continous set of observations made over the seasonal cycle of the vertical structure and currents in the Clyde Sea, Scotland's largest fjord, are used to show that the vertical structure is controlled by a balance between mixing and stratifying processes within the basin, and exchange with the North Channel of the Irish Sea. Stratification was observed to change from being entirely saline in the winter to being thermally dominated in the summer. Deep water renewal occurred throughout the winter. The inflow rate peaked in the early spring and also in the summer, resulting in an annual mean flushing time of -3.5 months, in satisfactory agreement with previous estimates. Within the basin, a two layered flow structure was observed throughout the year, and a residual anti-cyclonic surface circulation was seen to be persistent. A 3- dimensional modelling study supports the hypothesis that this flow is driven by currents associated with the density gradients at the basin's mouth. A positive density difference across the sill is a necessary but not sufficient condition for deep water renewal; when the difference was maximum in the winter, the rate of exchange was below average. Renewal was generally episodic, which is suggestive of wind induced exchange. The 3-dimensional model confirmed that changes in the wind direction could substantially increase or diminish exchange by enhancing or blocking the estuarine circulation. Rapid renewals in the spring time of 1993 and 1994 were initiated by storm events. In the summer of 1993, persistently high rates of exchange were observed. 3-dimensional modelling supported the hypothesis that this was due to the presence of saline water over the sill, which results from the summer time retreat of the front at the mouth of the Clyde Sea due to low freshwater inflow. An existing 1- dimensional filling-box model was developed in the light of the new observations. It showed that significant entrainment of Clyde Sea bottom water into this summer inflow was a possible mechanism to explain the deep water properties in the summer. Mixing was found to be predominantly wind driven. A positive correlation was found between the wind and the amplitude of intemal oscillations at sub-tidal frequencies, which dominated the velocity field in winter. A mode 1 internal tide at the M2 frequency was observed, and had a horizontal velocity at the mooring sites of -2 cms-l throughout the year. The mixing associated with the internal tide was -0.01 mWm-2 , which is 2 orders of magnitUde lower than the wind mixing. The residual surface anti-cyclonic circulation prevents surface fresh water from entering the Kilbrannan Sound, which reduces the potential energy anomaly by -60 Jm-) relative to than that of the Arran Deep. Consequently, the wind induces relatively deeper mixing in the Kilbrannan Sound, which in the winter resulted in the reduction of the bottom water temperature without a significant decrease in salinity, and explains how the Clyde Sea bottom water may cool more rapidly than the deeper North Channel.