Sea surface height (SSH) is routinely measured from satellites and used to infer ocean currents, including eddies, that affect the distribution of organisms and substances in the ocean. SSH not only reflects the dynamics of the surface layer, but also is sensitive to the fluctuations of the main pycnocline; thus it is linked to events of nutrient upwelling. Beyond episodic upwelling events, it is not clear if and how SSH is linked to broader changes in the biogeochemical state of marine ecosystems. Our analysis of 23 years of satellite observations and biogeochemical measurements from the North Pacific Subtropical Gyre shows that SSH is associated with numerous biogeochemical changes in distinct layers of the water column. From the sea surface to the depth of the chlorophyll maximum, dissolved phosphorus and nitrogen enigmatically increase with SSH, enhancing the abundance of heterotrophic picoplankton. At the deep chlorophyll maximum, increases in SSH are associated with decreases in vertical gradients of inorganic nutrients, decreases in the abundance of eukaryotic phytoplankton, and increases in the abundance of prokaryotic phytoplankton. In waters below ?100 m depth, increases in SSH are associated with increases in organic matter and decreases in inorganic nutrients, consistent with predicted consequences of the vertical displacement of isopycnal layers. Our analysis highlights how satellite measurements of SSH can be used to infer the ecological and biogeochemical state of open-ocean ecosystems.