State-space model decomposition of subsurface temperatures from the World Ocean Database is used to detect and characterize changes in thermal stratification in the upper 200 m of the California Current System (CCS) over the period 1950--1993. Model results are analyzed at eight locations representing the meridional and offshore extent of the CCS between 31¿N and 40¿N. Thermocline strength, depth, and temperature are derived from the mean-level trend term and the seasonal component of the state-space models. Over the 44 years, the mean level of the coastal thermocline strengthened and deepened, while it weakened and shoaled offshore. These tendencies are likely the result of geostrophic adjustment to changes in basin-scale circulation, as well as to a long-term increase in upper ocean heat content of 2--9% throughout the study area. Reduction in nutrient inputs to the surface layer resulting from these climate signals are a likely explanation for the pronounced decline in biological production in CCS ecosystems observed over the same period. Substantial decadal variability superimposed on these linear tendencies may play a role in determining the response of the upper ocean to interannual events such as El Ni¿o. The seasonal component of thermocline depth and strength exhibited a high degree of nonstationarity, with alternating periods of weakened and enhanced annual cycles lasting 3--5 years, along with changes in the phase. This changing seasonality may have implications for marine species whose life cycles are closely tuned to the seasonal cycle.