Inorganic carbon dynamics and their relation to autotrophic community regime shift over three decades in a large, alkaline river

How much of the excess CO2 in running waters comes from in‐stream respiration of organic carbon? To answer this, we developed a 30‐yr metabolism‐carbonate system database at an hourly resolution for the Loire River, France, a large, alkaline river. We asked the following questions: what are the intra‐annual patterns of in‐stream (“internal”) CO2 production, what processes drive these patterns, and how do these patterns depend on autotrophic community composition? We estimated internal CO2 production as the ratio of net ecosystem production to CO2 water‐to‐air flux (FCO2). We also estimated the daily ecosystem quotient (EQ, O2 released: dissolved inorganic carbon [DIC] consumed) and the prevalence of non‐CO2 autotrophic DIC uptake pathways under CO2 depletion. Median internal CO2 production was 49% of FCO2 in the Loire from 1990 to 2022. The river predictably shifted from a heterotrophic, CO2 source to an autotrophic, CO2 sink as a function of discharge, leading to four trophic‐flux (“trophlux”) states: autotrophic‐sink, autotrophic‐source, heterotrophic‐sink, and heterotrophic‐source. During autotrophic states (41% of the time), CO2 depletion (FCO2 ≤ 0, median pCO2 = 135 μatm) led to the use of and of CO2 released by CaCO3 precipitation as alternative DIC sources to autotrophs to support their high rates of primary production (occurring on average for 33% of the growing season). Finally, during a period of phytoplankton dominance, the median EQ was 1.3, which was reduced to 1.0 under macrophyte dominance. This work describes a dynamic coupling among autotrophic communities, calcium carbonate equilibria, and discharge‐controlled FCO2 that together imply lower‐than‐predicted FCO2 magnitude and greater‐than‐predicted internal CO2 production for the Loire River.