The goal of the Pacific Ocean Boundary Ecosystem and Climate Study (POBEX) was to diagnose the large-scale climate controls on regional transport dynamics and lower trophic marine ecosystem variability in Pacific Ocean boundary systems. An international team of collaborators shared observational and eddy-resolving modeling data sets collected in the Northeast Pacific, including the Gulf of Alaska (GOA) and the California Current System (CCS), the Humboldt or Peru-Chile Current System (PCCS), and the Kuroshio-Oyashio Extension (KOE) region. POBEX investigators found that a dominant fraction of decadal variability in basin- and regional-scale salinity, nutrients, chlorophyll, and zooplankton taxa is explained by a newly discovered pattern of ocean-climate variability dubbed the North Pacific Gyre Oscillation (NPGO) and the Pacific Decadal Oscillation (PDO). NPGO dynamics are driven by atmospheric variability in the North Pacific and capture the decadal expression of Central Pacific El Ninos in the extratropics, much as the PDO captures the low-frequency expression of eastern Pacific El Ninos. By combining hindcasts of eddy-resolving ocean models over the period 1950-2008 with model passive tracers and long-term observations (e.g., CalCOFI, Line-P, Newport Hydrographic Line, Odate Collection), POBEX showed that the PDO and the NPGO combine to control low-frequency upwelling and alongshore transport dynamics in the North Pacific sector, while the eastern Pacific El Nino dominates in the South Pacific. Although different climate modes have different regional expressions, changes in vertical transport (e.g., upwelling) were found to explain the dominant nutrient and phytoplankton variability in the CCS, GOA, and PCCS, while changes in alongshore transport forced much of the observed long-term change in zooplankton species composition in the KOE as well as in the northern and southern CCS. In contrast, cross-shelf transport dynamics were linked to mesoscale eddy activity, driven by regional-scale dynamics that are largely decoupled from variations associated with the large-scale climate modes. Preliminary findings suggest that mesoscale eddies play a key role in offshore transport of zooplankton and impact the life cycles of higher trophic levels (e.g., fish) in the CCS, PCCS, and GOA. Looking forward, POBEX results may guide the development of new modeling and observational strategies to establish mechanistic links among climate forcing, mesoscale circulation, and marine population dynamics.