Intertidal flats are highly productive coastal marine ecosystems which are affected by fast changes in environmental conditions and host dynamic biogeochemical cycles in their sediments. Bioturbation by burrowing organisms and roots of plants strongly affects speciation and cycling of redox-sensitive elements in intertidal sediments. In this work, we have studied the impact of sediment type and vegetation on the cycling of redox-sensitive elements including sulfur, iron, and manganese in sandy and muddy tidal flats sediments in the Jade Bay (North Sea) and adjacent area. The redox speciation of these elements was analyzed in the pore-waters and the total sediment. The isotopic compositions of sulfur species were measured in non-vegetated sediments and in sediments which are inhabited by various plants. In the cohesive sediments, which are not affected by vegetation, a decrease in sulfate concentration, coupled with the presence of relatively high concentrations of hydrogen sulfide in the pore-waters and the presence of sulfide minerals as well the isotopic compositions of sulfur species are consistent with fast rates of sulfate reduction in the sediments. In the cohesive sediments affected by roots of Salicornia stricta and sediments desiccation, a cryptic sulfur cycle, which is characterized by microbial sulfate reduction coupled to fast reoxidation of hydrogen sulfide by Fe(III) (hydr)oxides and, possibly, by oxygen is present. Below the roots penetration depth, speciation of redox-sensitive elements is similar to those in the baren sediments. In the cohesive sediments affected by the roots of Spartina anglica and Triglochin maritima, which have longer roots, a cryptic sulfur cycle was detected in the upper 30 cm of sediments. At the sites that are characterized by permeable surface sediments and alternating permeable and cohesive layers in the deeper sediments, the composition of the sediment has a similar or even more significant impact on the speciation of the redox-sensitive elements than penetration of relatively weak roots of Spartina anglica. These sediments are characterized by the formation of hydrogen sulfide and sulfide oxidation intermediates in the cohesive layers and their diffusion to (and oxidation at) the boundaries between cohesive and permeable sediments. We conclude that in the cohesive sediment, the penetration of roots and desiccation leads to the formation of overall oxidized conditions in the sediments, while in the sediments with alternating layers, permeability may provide a more significant control for speciation of redox-sensitive elements.