Sediment incubation studies mostly focus on a few target solutes. This approach provides a limited understanding of the interaction of the processes behind the different solutes occurring in sediments. We provide here a comprehensive data set that covers many solutes to enable a better understanding of the important processes in the sediments. The sediment incubation results in this data set were collected from five water bodies; Hassel pre-dam in 2013, Rappbode pre-dam in 2014, Rappbode Reservoir in 2015, Bautzen Reservoir in 2014, and Sau Reservoir in 2015. The data is divided into 5groups;i. CTD/Sonde profiles (depth, temperature, dissolved oxygen, pH, turbidity, and chlorophyll-a.ii. Sediment incubation fluxes at different in-situ oxygen and conditions; dissolved organic carbon, methane, nitrate, ammonium, sulphate, dissolved iron and dissolved manganese. Sediments were collected using a gravity sampler (Uwitec, Mondsee, Austria).iii. Porewater concentration; dissolved organic carbon, methane, sulphate, dissolved iron and dissolved manganese. Porewater was extracted by centrifugation.iv. Sediment characterization; loss on ignition, water content, total carbon, total organic carbon, and total iron.v. Calculated parameters; Fred (total oxygen required per area to oxidize all reduced compounds released by the sediment), and respiration