This data set contains data from water analyses from column experiments. The water analyses included cations (sodium, potassium, calcium, magnesium, iron and manganese), anions (nitrate, chloride, sulphate, bromide and phosphate) and selected trace elements (arsenic, cobalt, nickel, vanadium and zinc). The column experiments were conducted with two different types of unconsolidated sandy sediments from aquifers in Denmark (Quaternary) and Germany (Cretaceous). In both sediments, the nitrate degradation capacity was almost exhausted. To induce denitrification, 5 mmol ethanol was added to the column experiments. This also caused a decrease in the concentration of trace elements in the water. A sequential extraction procedure was performed to determine the trace element sinks. The data set therefore also contains contents of selected elements (equal to water analyses) from the sequential extraction procedure of the sediment before and after the column tests. The results observed in the laboratory were additionally modeled with Phreeqc. The Phreeqc input data complete the data set.