In coastal marine systems worldwide, land‐based nutrient inputs are often correlated with blooms of macroalgae, which can negatively affect seagrass habitats. We used spatiotemporal trends in production to identify the role of marine‐derived nutrients in mediating these interactions. Among ocean upwelling‐influenced estuaries along the northeastern Pacific, we documented a negative correlation between annual production of ulvoid macroalgae and the seagrass, Zostera marina L., at a regional scale that included four estuaries along a ∼ 400 km distance. While macroalgal biomass was ∼ 30 times greater in southern (Yaquina Bay and Coos Bay, Oregon) compared to northern (Willapa Bay, Washington, and Netarts Bay, Oregon) estuaries, no temporal patterns of eelgrass decline were observed within the estuaries over a 5 yr period. Latitudinally, 65% of the between‐site ordination variance in interannual macrophyte production was associated with ocean upwelling; macroalgae was positively correlated, and eelgrass negatively correlated with more intense upwelling. Within one estuary, Coos Bay, we found that land‐based nutrients had no effect on macrophyte productivity. Instead, a little more than a third of the variation was explained by upwelling (marine dissolved inorganic nitrogen and salinity) and climate (photosynthetically active radiation). Thus, contrary to the paradigm of negative effects of macroalgae on eelgrass, we found correlative evidence that ocean upwelling and local estuarine conditions could be responsible for these large biogeographic patterns.