The seasonal variation of the physical characteristics and of large-scale current patterns of the California Current system is examined using harmonic analysis applied to the 23 years of California Cooperative Oceanic Fisheries Investigations data collected between 1950 and 1978. The amplitude and phasing of seasonal variation in dynamic height and the overall standard deviation of dynamic height define three domains: oceanic, coastal, and an intervening transition zone. The transition zone is a broad band centered approximately 200–300 km offshore and parallel to the coast in which the seasonal range of dynamic height is a relative minimum and the standard deviation is a maximum. It is hypothesized that recurrent mesoscale eddies and energetic meanders create this zone. Such eddies and meanders would contribute heavily to the standard deviation of dynamic height but not its seasonal variation. The transition zone is coincident with the core of flow of the California Current. A strong interaction between the core of the California Current and the mesoscale eddy field is evident. Seasonal variation in the fields of temperature, salinity, σt, and oxygen is related to variations in the California Current, the Inshore Countercurrent and the California Undercurrent through vertical adjustments in the density field and through changes in transport. In the undercurrent there is an especially strong relation between seasonal variations in strength of flow and the extreme values of water mass characteristics.