The effects of salinity intrusion on the anaerobic microbial and geochemical dynamics of tidal freshwater sediments were investigated using flow-through sediment reactors. In freshwater control sediments, organic matter mineralization was dominated by methanogenesis (62%), followed by sulfate reduction (18%), denitrification (10%), and iron reduction (10%). Upon salinity intrusion, nutrient (ammonium, silicate, phosphate) concentrations increased and rates of methanogenesis declined. Iron-oxide bioavailability increased and microbial iron reduction appeared to account for >60% of organic matter oxidation for several days after salinity intrusion. However, sulfate reduction was the dominant pathway (>50%) of organic matter oxidation within 2 weeks of salinity intrusion, and accounted for >95% of total organic matter mineralization after 4 weeks. Total in situ sediment organic matter mineralization doubled following salinity intrusion. Increased nutrient release, decreased methanogenesis and a rapid shift to sulfate reduction, with a coincident increase overall organic matter mineralization, accompanied salinity intrusion into previously freshwater riverine sediments.