A comparison of fluxes of ten dissolved constituents of rain water and river water has been carried out for the watershed of the Apalachicola River in order to estimate the magnitude of nitrate contribution from the atmosphere to surface water that may flow to the Apalachicola Bay estuary. The comparison is based on statistical analysis of both atmospheric and fiver water monitoring data: weekly rain water chemical data from the National Acid Deposition Program (NADP) for five sites within the watershed area, from 1978–84 until late 1989, and less frequent river water chemical data from the U.S. Geological Survey for one site ai Chattahoochee, Florida, from 1965 until late 1989. The means and standard errors of the fluxes from the atmosphere and in the river flow were determined. As a measure of correlations between different ionic concentrations in the rain and river water data sets, factor analysis was used to account for data variance by a sum of principal components according to a linear mixing model. By comparing the compositions and magnitudes of these components, judgments could be made concerning the importance of atmospheric deposition as a source of nitrate in the watershed as well as of chemical transformations and possible loss of nitrate during its residence in the watershed and transport to the estuary. Although surface sources of N and extent of loss to the atmosphere by denitrification have not yet been quantitatively determined, atmospheric deposition to the watershed appears to be sufficient to account for essentially all the dissolved nitrate and ammonium and total organic N flow in the river. After deposition most of the nitrate may be transformed to other chemical forms during the flow, except possibly under high flow conditions that mainly occur in winter. However, either nitrate or the other forms could, with high efficiency, reach the estuary and be available for its marine biological processes.