The study of manganese (Mn) and iron (Fe) cycling in early diagenetic processes in estuaries is crucial for understanding the functioning of these vital ecosystems and predicting their responses to environmental change. The present study investigates the dynamic interplay of Mn and Fe in early diagenetic processes at highly contrasted hydrosedimentary conditions in the Loire estuary, which is very rare and allows a comprehensive framework to understand diagenetic processes in a very dynamic environment. One campaign took place in the Brillantes intertidal mudflat in March 2015 (PV1), while 3 others took place in a muddy riverbed along the navigation channel off the city of Paimboeuf during a decennial flood in February (RR1–4), under moderate discharge in June (RRK-4) and low in August 2021 (RR2–4). The monitored riverbed station was upstream, under and downstream the maximum turbidity zone, respectively. By combining sequential extraction techniques for Mn and Fe in solid phases and pore-water analysis, the study provides insights into the behaviour of these elements in sedimentary environments and reveals their speciation and association with specific mineral phases and forms during different diagenesis stages. The remobilization of Mn and Fe in the surface sediments of the Brillantes mudflat (PV1) allows iron sulphide formation within the upper 50 cm of the sediment column (above the sulphate penetration depth). The deeper layers show other authigenic phases formation, such as the probable precipitation of vivianite below the sulphate depletion depth and progressive precipitation of carbonate at depth, leading to definitive burial and accumulation. At the muddy riverbed, following the exceptional flood in February 2021 (RR1–4), significant sediment erosion occurred unveiling to the water column old and reduced sediments. Sharp pore-water gradients for dissolved Mn, Fe and sulphate indicated the sudden exposure of the old 7Be-free and anoxic sediment to low-salinity, well‑oxygenated water. Despite its dark colour, this sediment showed no authigenic FeS/FeS2 phases. Four months later, changes in the estuarine environment (low river discharge) and the presence of a maximum turbidity zone (TMZ) led to a new deposition of a sediment layer (RRK-4) triggering transient diagenetic reactions. The freshly deposited sediment layer developed important recycling of dissolved Mn, Fe and sulphate above the precedent sediment water interface (SWI) generating a double peak, accompanied by consistently low concentrations of solid Mn and Fe phases specially FeS/FeS2 and Mn bound to FeS/FeS2 compared to PV1. Six months after the flood event, in August (RR2–4), the discernible attenuation of dissolved Mn and Fe peaks and sulphate concentration, indicated a gradual recovery of characteristic sediment profiles with the well-known redox layer succession. Overall, despite important sulphate reduction within sediments from both the river and its adjacent mudflats, pyritization is not a major process for Mn and Fe burial. The intense hydrodynamics of the mid estuary prevents thermodynamical equilibrium between pore-water chemistry and solid phases not allowing pyrite formation while in the calmer conditions of intertidal mudflats, pyrite accumulates in intermediate depths but carbonates and phosphates seem to be the preferential phases of burial probably related to methane production and phosphate availability.