Information on water balances and water composition for groundwater in a crystalline rock terrain and mountainous topography that make abrupt inflows into a receiving river water is rare. Furthermore, it is unusual to have groundwater of quite different composition from river water composition so that it is easily detectable. Such data were collected in 2001 and 2002 as part of a project to determine transport and properties of naturally occurring acid sulfate groundwaters in the mineralized area of the Red River Valley, New Mexico. Two tracer-injection studies with synoptic sampling were conducted for the Red River these low flow conditions and monitoring of several wells and surface waters provided chemical data for the river and the groundwaters. A sulfate mass flux model was constructed based on estimates of water yield for this portion of the basin and sulfate concentrations. Assuming the water balance is well established and the most certain data are the fluvial sulfate mass fluxes, a model was constructed assuming an average groundwater sulfate concentration of 400 mg/L. Yields gave total flows from side catchments, and sulfate fluxes in the river above and below acid inflows were measured. This model gave a reasonable accounting of mass fluxes but when the concentration of sulfate from emerging and non-emerging groundwaters were compared, they were not the same and that seemed unlikely unless there was incomplete mixing. This model, called model 1, was revised so that these two sulfate concentrations were the same (i.e. complete mixing), and the sulfate concentrations in the catchment groundwaters were adjusted so that the sulfate fluxes still balanced and this became model 2. A third model was constructed that assumed the inflow sulfate flux in the fluvial sediment was incorrect and that the other assumptions are reasonable. This value was adjusted leaving other parameters as in model 2. Although there are several sources of uncertainties, at least some bounding constraints on the range of sulfate fluxes for natural sources could be estimated before downstream contamination from mining activities occurred. The influx of upstream natural acidic flows were comparable to the flows of sulfate and other contaminants coming from the mine site downstream regardless of model type.