A likely consequence of sea level rise during the next century will be progressive inundation of seawater through the current unsaturated zone in coastal-margin soils. It is unclear how this will change the biogeochemical cycling of iron, sulfur and carbon over different time scales and soil types. A long-term (540 day) laboratory experiment, slowly inundating intact coastal soil cores with seawater from the ‘bottom up’, was conducted to observe how coupled iron and sulfur dynamics change in different soil types. Pore water was extracted from the 60 cm cores at 10 cm depth intervals every 90 days and analysed for pH, electrical conductivity (EC), Fe2+, HS− and dissolved metals (Fe, Mn, As, Cd, Cu, Ni, Pb, Co, Zn) as well as stable sulfur (34S/32S) and radiogenic strontium (87Sr/86Sr) isotopes. Destructive solid phase analyses (for reactive Fe, acid volatile and chromium reducible sulfur (AVS and CRS) and total organic carbon (TOC)) were made at the start and end of the experiment. Iron and sulfate reduction was induced in soils with readily available TOC as anoxic conditions established, evidenced by statistically significant increases (P < 0.001) in dissolved Fe2+ and sulfide concentrations in porewaters, as well as simultaneous and progressive increase in the sulfur isotope (34S/32S) ratios. An increase in AVS indicated formation of metastable iron sulfide (FeS) minerals resulting from Fe2+ and sulfide in porewaters post inundation. This was supported by PHREEQC modelling of local mineral saturation states/indices in the system. Overall, the Fe2+ concentration increased to a peak at between 270 and 360 days, and then began decreasing at some depths, indicating slowing iron reduction, presumably because reactive iron (oxyhydro)oxides became progressively consumed by microbially driven reductive processes. However, microbially mediated sulfate reduction continued as abundant sulfate was still available from seawater. In the absence of free Fe2+, sulfide accumulated in the porewater, but only in those soils inundated the longest (>360 days), and with greater than 5% TOC. The combined use of sulfur (34S/32S) and strontium (87Sr/86Sr) isotopes supported the observed results, and represents a new and robust technique to quantify progressive sulfate reduction and seawater mixing phenomena in coastal soils. This study gives new insights into the biogeochemical cycling of sulfur and iron in soils experiencing seawater inundation from sea level rise over longer timescales. It is likely that sulfidisation (due to in-situ sulfate reduction) will begin to affect coastal wetland soils, especially in areas where TOC is high and where reactive iron depletes over time. This has potential consequences for sulfide toxicity in coastal soils and environments globally.