Here we show an analysis of river flow and water chemistry data from eleven gauging stations along the Pecos River in eastern New Mexico and western Texas, with time spanning 1959--2002. Analysis of spatial relationship between the long-term average flow and total dissolved solids (TDS) concentration allows us to illuminate four major processes controlling river chemistry, namely saline water addition, evaporative concentration with salt gain or loss, dilution with salt gain or loss, and salt storage. Of the 10 river reaches studied, six reaches exhibit the process dominated by evaporative concentration or freshwater dilution with little change in salt load. Four reaches show considerable salt gains or losses that are induced by surface-ground water interactions. This analysis suggests that the evaporative concentration and freshwater dilution are the prevailing mechanisms, but local processes (e.g., variations in hydrologic flowpath and lithologic formation) also play an important role in regulating the hydrochemistry of the Pecos River.