Dissolved organic matter (DOM) helps regulate aquatic ecosystem structure and function. In small streams, DOM concentrations are controlled by transport of terrestrial materials to waterways, and are thus highly variable. As rivers become larger, the River Continuum Concept hypothesizes that internal primary production is an increasingly important DOM source, but direct evidence is limited. Recently, the Pulse-Shunt Concept postulated that terrestrial DOM concentrations in larger rivers increase with flow and temperature, which seemingly contradicts previously reported DOM chemostasis in large rivers. This study estimates daily gross primary production (GPP) in 13 streams and rivers across the Connecticut River watershed (watershed areas 0.4–25,019 km²) from 2015 through 2017. Chemostasis of DOM concentrations is maintained by a switch from autochthonous sources of DOM at low flows to terrestrial sources of DOM at high flows in a large temperate river and to a lesser degree in smaller tributaries. At low flow, autochthonous DOM linked to aquatic GPP is the dominant fraction of the DOM pool in large rivers. This autochthonous DOM maintains chemostasis in the main stem and to a lesser extent upstream. Thus, in larger rivers, low-flow autochthonous production stabilizes DOM concentrations during the summer, a critical time for riverine ecology. Consistent with the Pulse-Shunt Concept, terrigenous DOM is the dominant fraction of DOM during higher flow periods and about 70% of annual DOM fluxes to the coast are terrestrial. This pattern of DOM switching is potentially widespread in temperate watersheds with implications to both inland waters and coastal ecosystems.