The North Pacific Subtropical Gyre (NPSG) has experienced sustained warming and biological change in recent decades, yet how these changes through the water column are less well resolved. Here, we combined satellite observations from 1998–2024 with physical and biogeochemical Argo data and a long-term record from Station ALOHA to examine changes across the upper 300 m. Surface chlorophyll declined as sea-surface temperature increased. A marked physical transition around 2013–2014 involved changes in mixed-layer depth, ocean heat content, density structure, and the separation between the mixed layer and euphotic-zone depth. Subsequent biological changes were strongly depth-dependent, with chlorophyll declining most in the 75–105 m range, and the deep chlorophyll maximum deepened despite a comparatively stable euphotic-zone depth. These chlorophyll changes did not translate directly into changes in phytoplankton carbon biomass. In the upper water column, recent carbon biomass increased even as chlorophyll declined, while increases in chlorophyll relative to carbon at depth suggested that the deepening chlorophyll maximum did not simply represent a deeper biomass maximum. Station ALOHA observations also revealed depth-dependent changes in phytoplankton community composition that may have added to these patterns. Together, these results show that long-term warming in the NPSG has occurred alongside a reorganization of upper-ocean physical structure and phytoplankton vertical distribution, rather than a uniform decline in phytoplankton biomass through the water column.