Reactions occurring on the surfaces of biogenic carbonate minerals can have important consequences for the biogeochemical cycle of carbon. In this study, carbonate mineral surface reactions with ambient seawater were investigated by atomic force microscopy (AFM). A sampling method was developed in which calcite surfaces were hung at discrete depths on a sediment trap array line for a three-day deployment period in subtropical North Pacific waters. Changes in surface morphologies were examined at nanometer resolution and evaluated using as a constraint the depth profile of calcite saturation in these waters. Evidence suggests that: (1) organic films which develop on carbonate surfaces exposed to shallow seawater may be responsible for the oversaturated state of the upper oceanic water column, (2) dissolution of carbonate minerals within the shallow warm layer of the ocean could be responsible for part of the alkalinity anomaly observed in the North Pacific.