The research of his group is primarily concerned with the biogeochemical behavior and cycling of essential and potentially toxic trace elements in terrestrial and semi-terrestrial systems, and the coupling of these elements to the biogeochemistry of iron, manganese and sulfur. Currently, his group focuses on the biogeochemistry of metals and metalloids in periodically flooded or water-saturated soils, such as contaminated river floodplains and irrigated rice paddies, where plant uptake of cadmium and arsenic pose important problems.

Ruben Kretzschmar has authored or co-authored more than 150 research articles in peer-reviewed scientific journals, several review articles and book chapters, and one of the leading textbooks in Soil Science.