Concentrations of dissolved and particulate organic carbon (DOC and POC), total suspended solids (TSS), were measured daily, and phytoplankton pigments (chlorophyll-a and pheopigments) were measured every 3 days at three strategic stations along the eutrophic Loire River between November 2011 and November 2013 marked by a high annual and seasonal variability in hydrological regimes. This unique high-frequency dataset allowed to determine the POC origin (autochthonous or allochthonous). Some strong relationships were evidenced between POC, total pigments and TSS and were tested on a long-term database with a lower frequency (monthly data) to reconstitute unmeasured algal and detrital POC concentrations and estimate annual total organic carbon (TOC) fluxes from 1980 onwards. The results were subjected to only ≈25 % uncertainty and showed that the annual TOC fluxes at the outlet of the Loire River decreased from 520 103 tC year−1 (i.e. 4.7 t km−2 year−1) in the early 1990s to 150 103 tC year−1 (i.e. 1.4 t km−2 year−1) in 2012. Although DOC always dominates, the autochthonous POC represented 35 % of the TOC load at the basin outlet by the end of the 1980s and declined to finally represent 15 % only of the TOC. The control of phosphorus direct inputs and the invasion by Corbicula clams spp. which both occurred since the early 1990s probably highly reduced the development of phytoplankton. Consequently, the autochthonous POC contribution declined and TSS concentrations in summertime significantly decreased as well as a result of both less phytoplankton and less calcite precipitation. At the present time, at least 75 % of the POC has allochthonous origins in the upper Middle Loire but downstream, autochthonous POC dominates during summer phytoplanktonic blooms when total pigments concentrations reach up to 70 μg L−1 (equivalent to 75 % of the total POC).