To understand role of biogeochemical reactions in controlling the amount and molecular form of dissolved carbon exported from carbonate terrains, spatiotemporal variations in dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) were observed over one year in the Santa Fe River system, a period of base flow or below. A water mixing model developed using concentrations of Na ? , Cl -, and SO 4 -2 identified three major water sources: soil water, groundwater and deep aquifer water. After accounting for mixing of these water sources, additional chemical signatures resulting from biogeochemical processes in the riparian zone were identified. Net mineralization of DOC occurred throughout the Santa Fe River watershed, particularly during the lowest flow conditions and in the upper watershed. However, natural dissolved organic matter was more labile during low flow and in the lower watershed, and predominantly derived from groundwater (rather than soil water) in all samples, likely via releases during carbonate dissolution. Carbonate dissolution commonly occurred in the upper watershed during low flow conditions, while carbonate minerals precipitated during baseflow, as well as in the lower watershed during very low flow conditions. Thus, riparian zone biogeochemical processes were strongly mediated by watershed hydrology, whose spatiotemporal variations resulted in greater inorganic and organic C export production in the lower watershed than the upper watershed, and during higher flow versus lower flow periods. During this lower flow period, the Santa Fe River watershed exported *1.0 and 10.3 ton km -2 year -1 DOC and DIC, respectively, representing higher C yields than many other types of watersheds.