This dataset includes chemical, discrete samples and profile observations data collected from Canadian Coast Guard Ship John P. Tully in the North Pacific Ocean, coastal upwelling region west of Vancouver Island, Canada from 1998-07-15 to 1998-07-23. These data include dissolved inorganic carbon (DIC), total alkalinity (TA), temperature, salinity, dissolved oxygen, silicate, nitrate and phosphate. The inner-shelf buoyancy current, the outer-shelf and the slope regions are contrasted for both wind regimes (up- and downwelling). Results show strong biological drawdown of the partial pressure of carbon dioxide (pCO2) in response to upwelling over the outer-shelf. In contrast, measured pCO2 is exceptionally high (pCO2>1000ppm) in the inner-shelf current, where biological uptake of carbon is consistently large. The biological C:N uptake ratio appears to increase when nitrogen becomes limiting (during downwelling), while the POC:PON ratio is relatively constant (slightly lower than the Redfield ratio) suggesting that excess carbon uptake does not go into the POC pool. As expected, large cells dominate where measured primary productivity is greatest. Sub-surface inorganic carbon (and pCO2) is high over the shelf. We suggest that carbon concentrations may be higher in coastal waters because of remineralization associated with high productivity that is confined to a smaller volume of water by bathymetry. At the coast these sub-surface concentrations are more efficiently mixed into the surface (especially during winter) relative to deeper offshore regions. Thus, despite high primary production, coastal waters may not aid in sequestration of atmospheric carbon.