State-space models are applied to 13 years of monthly satellite-measured chlorophyll concentrations of the California Current, from British Columbia to Baja California, to isolate the slowly varying background trend from potentially nonstationary seasonal cycles, other higher-frequency cyclical variability, and an irregular plus measurement error signal. Temporal patterns in resulting background trends cluster into four dominant groups, three of which have increasing trends, the strongest of which extends over the coastal upwelling region from southern Oregon to Point Conception, California, and has a mean of 0.118 mg CHL m−3 decade−1. Overall, statistically significant increasing trends are observed over 75% of the study area, 20% of the study area had no trend, and 5% showed decreasing chlorophyll. Location-specific trend estimation shows increases are strongest (> 0.2 mg CHL m−3 decade−1) in upwelling areas along the Washington, Oregon and central California coasts, weaker in regions > 200 km offshore, and that positive trends are statistically significant over most of the California Current north of ∼27°N. Negative trends are evident south of ∼31°N off Baja California. These trends remain significant with similar spatial pattern, but lower magnitude, when the 1997–1998 El Niño period is removed from the analysis. State-space models of trends in alongshore wind stress and sea surface temperature over the same period indicate that local mechanisms linked to these chlorophyll trends are not clear. Comparisons of the chlorophyll trends to nonlocal signals, characterized by the North Pacific Gyre Oscillation and the Multivariate El Niño Index, map the spatially varying ecological footprint of these basin-scale signals.