The Clyde Sea is a deep, partially enclosed basin on the West Coast of Scotland which communicates with the adjacent North Channel of the Irish Sea via exchange flow over a relatively shallow entrance sill. The basin receives large inputs of nutrient rich freshwater which induces a reduction in surface salinities of up to 1.5 psu and maintains almost continuous stratification. Time series data collected in the area show a well defined seasonal cycle of stratification which has previously been explained with the aid of a one-dimensional filling box model. This model has been extended to examine the extent to which the observed seasonal cycles of nitrate and chlorophyll can be explained by the stepwise inclusion of additional non-conservative terms. The results show that, as a result of the interaction between the physical and biological seasonal cycles, nitrate accumulates in the Clyde Sea during the summer, which is then supplied to the North Channel of the Irish Sea during the winter and spring.