We study the marine and terrestrial contributions in the Gulf of California (GC) to understand the relationship between continental climate and oceanographic variability over the last 28 ka. In Core AII125‐8‐JPC‐20, we examine aeolian and riverine inputs as nutrients for biological productivity. We use biogenic silica (%opal), total organic carbon (%TOC) and calcium carbonate (%CaCO3) as proxies for primary productivity, and lithic fraction distributions as proxies for terrigenous transport. At the core site, biogenic and lithic components are in phase at millennial‐scale in response to regional climate conditions. During the Late Pleistocene, the GC shelf area was above sea level and the western margin showed transient episodes of increased fluvial inputs. Episodic increases in %opal and reduced %TOC suggest upwelling events but ineffective C‐export to the sediment. During stadial events (Heinrich 2, Heinrich 1, Younger Dryas), regional declines in %opal, but increases in %CaCO3 and TOC, suggest efficient C‐export by carbonate organisms. During most of the Holocene, dust inputs are higher. Episodic increases in %TOC suggest higher C‐accumulation, although this is not controlled by siliceous or calcareous organisms. In the GC, besides upwelling and current advection, nutrient inputs driven by terrestrial climate have an impact on the biological C‐pump. © 2020 John Wiley & Sons, Ltd.