We examined the solubility, mineralogy and geochemical transformations of sedimentary Fe in waterways associated with coastal lowland acid sulfate soils (CLASS). The waterways contained acidic (pH 3.26–3.54), Fe III-rich (27–138 μM) surface water with low molar Cl:SO 4 ratios (0.086–5.73). The surficial benthic sediments had high concentrations of oxalate-extractable Fe(III) due to schwertmannite precipitation (kinetically favoured by 28–30% of aqueous surface water Fe being present as the Fe III SO 4 + species). Subsurface sediments contained abundant pore-water HCO 3 (6–20 mM) and were reducing (Eh < −100 mV) with pH 6.0–6.5. The development of reducing conditions caused reductive dissolution of buried schwertmannite and goethite (formed via in situ transformation of schwertmannite). As a consequence, pore-water Fe II concentrations were high (>2 mM) and were constrained by precipitation–dissolution of siderite. The near-neutral, reducing conditions also promoted SO 4-reduction and the formation of acid-volatile sulfide (AVS). The results show, for the first time for CLASS-associated waterways, that sedimentary AVS consisted mainly of disordered mackinawite. In the presence of abundant pore-water Fe II, precipitation–dissolution of disordered mackinawite maintained very low (i.e. <0.1 μM) S −II concentrations. Such low concentrations of S −II caused slow rates for conversion of disordered mackinawite to pyrite, thereby resulting in relatively low concentrations of pyrite (<300 μmol g −1 as Fe) compared to disordered mackinawite (up to 590 μmol g −1 as Fe). This study shows that interactions between schwertmannite, goethite, siderite, disordered mackinawite and pyrite control the geochemical behaviour of sedimentary Fe in CLASS-associated waterways.