A new model for three-dimensional mesoscale flow is used to simulate the vertical transport of nutrients into the euphotic zone from deeper waters. We use the model to diagnose the effects of mesoscale motions on the upper ocean biogeochemical cycles of NO3, CO2, O2, sea surface exposure tracers that resemble dissolved organic carbon (DOC) and H2O2, and the corresponding rates of new production and gas exchange in regions near the Joint Global Ocean Flux Study (JGOFS) oligotrophic time series sites of Hawaii and Bermuda during late summer. The physical model is nonhydrostatic and designed to handle open boundaries without excessive damping as described by Mahadevan and Archer <1998>. It is initialized and driven at the open boundaries with flow fields from the 1/4¿ global circulation model of Semtner and Chervin <1992>. We examine the effect of model resolution and the attending increase in mesoscale and frontal-scale motions on the nutrient and carbon chemistry of the upper ocean. New production, approximated and diagnosed as an exponential uptake of nutrients within the euphotic zone, increases with model resolution. Nutrient is supplied for new production where isopycnals from the subsurface outcrop at the base of the euphotic zone, primarily at fronts. The rate and spatial scale of upwelling and nutrient uptake are more sensitive to model resolution than are temperature or the more slowly responding geochemical tracers such as CO2. ¿ 2000 American Geophysical Union