Three sediment stations in Himmerfjärden estuary (Baltic Sea, Sweden) were sampled in May 2009 and June 2010 to test how low salinity (5–7 ‰), high primary productivity partially induced by nutrient input from an upstream waste water treatment plant, and high overall sedimentation rates impact the sedimentary cycling of methane and sulfur. Rates of sediment accumulation determined using 210Pbexcess and 137Cs were very high (0.65–0.95 cm year−1), as were the corresponding rates of organic matter accumulation (8.9–9.5 mol C m−2 year−1) at all three sites. Dissolved sulfate penetrated <20 cm below the sediment surface. Although measured rates of bicarbonate methanogenesis integrated over 1 m depth were low (0.96–1.09 mol m−2 year−1), methane concentrations increased to >2 mmol L−1 below the sulfate–methane transition. A steep gradient of methane through the entire sulfate zone led to upward (diffusive and bio-irrigative) fluxes of 0.32 to 0.78 mol m−2 year−1 methane to the sediment–water interface. Areal rates of sulfate reduction (1.46–1.92 mol m−2 year−1) integrated over the upper 0–14 cm of sediment appeared to be limited by the restricted diffusive supply of sulfate, low bio-irrigation (α = 2.8–3.1 year−1), and limited residence time of the sedimentary organic carbon in the sulfate zone. A large fraction of reduced sulfur as pyrite and organic-bound sulfur was buried and thus escaped reoxidation in the surface sediment. The presence of ferrous iron in the pore water (with concentrations up to 110 μM) suggests that iron reduction plays an important role in surface sediments, as well as in sediment layers deep below the sulfate–methane transition. We conclude that high rates of sediment accumulation and shallow sulfate penetration are the master variables for biogeochemistry of methane and sulfur cycling; in particular, they may significantly allow for release of methane into the water column in the Himmerfjärden estuary.