Trends and seasonality analysis from 1980 onward and longitudinal distribution, from headwaters to estuary, of chlorophyll a, nitrate and phosphate were investigated in the eutrophic Loire River. The continuous decline of phosphate concentrations which has been recorded since 1991 both in the main river and in the tributaries has led to the conclusion that it was responsible for the significant reduction in phytoplanktonic biomass across the whole river system, although Corbicula spp. clams invaded the river during the same period and probably played a significant role in the phytoplankton decline. While eutrophication remained lower in the main tributaries than in the Loire itself, they were found to contribute up to ≈ 35% to the total nutrient load of the main river. The seasonality analysis revealed significant seasonal variations for the different eutrophication metrics and calls into question the classical monthly survey recommended by national or international authorities. Reducing P inputs impacted these seasonal variations: the decline of seasonal amplitudes of chlorophyll a reduced the seasonal amplitude of orthophosphate and of daily variations of dissolved oxygen and pH but did not significantly affect the seasonal amplitude of nitrate. Thus, the influence of phytoplankton on seasonal variations of nitrate was minor throughout the period of study.

To allow climate change impact assessment of water quality in river systems, the scientific community lacks efficient deterministic models able to simulate hydrological and biogeochemical processes in drainage networks at the regional scale, with high temporal resolution and water temperature explicitly determined. The model QUALity-NETwork (QUAL-NET) was developed and tested on the Middle Loire River Corridor, a sub-catchment of the Loire River in France, prone to eutrophication. Hourly variations computed efficiently by the model helped disentangle the complex interactions existing between hydrological and biological processes across different timescales. Phosphorus (P) availability was the most constraining factor for phytoplankton development in the Loire River, but simulating bacterial dynamics in QUAL-NET surprisingly evidenced large amounts of organic matter recycled within the water column through the microbial loop, which delivered significant fluxes of available P and enhanced phytoplankton growth. This explained why severe blooms still occur in the Loire River despite large P input reductions since 1990. QUAL-NET could be used to study past evolutions or predict future trajectories under climate change and land use scenarios.

In freshwater ecosystems, dynamic hydraulic events (floods or dam maintenance) lead to sediment resuspension and mixing with waters of different composition. Microbial communities living in the sediments play a major role in these leaching events, contributing to organic matter degradation and the release of trace elements. However, the dynamics of community diversity are seldom studied in the context of ecological studies. Therefore, we carried out laboratory-induced leaching experiments, using sediments from the Villerest dam reservoir (Villerest, France). To assess whole microbial community diversity, we sequenced the archaeal and bacterial 16S rRNA genes using Illumina MiSeq. Our results suggest that the degree of dissolved oxygen found in the water during these resuspension episodes influenced community dynamics, with anoxic waters leading to drastic shifts in sedimentary communities compared to oxic waters. Furthermore, the release of microbial cells from sediments to the water column were more favorable to water colonization when events were caused by oxic waters. Most of the bacteria found in the sediments were chemoorganotrophs and most of the archaea were methanogens. Methylotrophic, as well as archaeal, and bacterial chemoorganotrophs were detected in the leachate samples. These results also show that organic matter degradation occurred, likely participating in carbonate dissolution and the release of trace elements during freshwater resuspension events.

To avoid the improper disqualification of a watershed for which the water–rock interaction (WRI) may produce trace element concentrations exceeding established guidelines, it is of the utmost importance to properly establish natural geochemical backgrounds. Using the example of the crystalline Upper Loire River Basin, we are proposing a methodology based on the selection and chemical characterization of water and sediment samples from 10 monolithologic watersheds supposedly lowly impacted by anthropogenic inputs. We collected water samples from each watershed’s spring down to its outlet and measured dissolved major, minor and selected trace elements (Al, As, Ba, Cd, Co, Cr, Cs, Cu, La, Ni, Pb, U, V and Zn) at low- and high-water stages. Results show that the chemical signature of the stream waters is controlled by mineral weatherability rather than by the available rock stock. As a result, the variability in dissolved metal concentrations between the principal lithologies is similar to that observed within each of them. While some elements mostly result from WRI, others clearly identify high inputs from topsoil leaching. Comparison with published data evidences the need to subdivide studied watersheds into distinct sectors, according to the distance from the spring, in order to define reliable natural backgrounds.