Drought is common in rivers, yet how this disturbance regulates metabolic activity across network scales is largely unknown. Drought often lowers gross primary production (GPP) and ecosystem respiration (ER) in small headwaters but by contrast can enhance GPP and cause algal blooms in downstream estuaries. We estimated ecosystem metabolism across a nested network of 13 reaches from headwaters to the main stem of the Connecticut River from 2015 through 2017, which encompassed a pronounced drought. During drought, GPP and ER increased, but with greater enhancement in larger rivers. Responses of GPP and ER were partially due to warmer temperatures associated with drought, particularly in the larger rivers where temperatures during summer drought were > 10°C higher than typical summer baseflow. The larger rivers also had low canopy cover, which allowed primary producers to take advantage of lower turbidity and fewer cloudy days during drought. We conclude that GPP is enhanced by higher temperature, lower turbidity, and longer water residence times that are all a function of low discharge, but ecosystem response in temperate watersheds to these drivers depends on light availability regulated by riparian canopy cover. In larger rivers, GPP increased more than ER during drought, even leading to temporary autotrophy, an otherwise rare event in the typically light‐limited heterotrophic Connecticut River main stem. With climate change, rivers and streams may become warmer and drought frequency and severity may increase. Such changes may increase autotrophy in rivers with broad implications for carbon cycling and water quality in aquatic ecosystems.