The Department of Ecosystem Biology provides a Bachelors programme in Environmental Management. The department also provides a Masters programme in Ecosystem biology, in which students specialize in Ecology, Hydrobiology, Soil Biology, Applied Ecology and Biology of Nature Conservation. These programmes are conducted in Czech. The department also offers two PhD programmes in Czech or English, Ecosystem Biology and Hydrobiology.

Research at the department includes independent projects as well as collaborations with the Institute of Hydrobiology, Institute of Entomology and Institute of Soil Biology of the Biologe Centre AS CR and the Třebon branch of the Institute of Botany AS CR. We also have ongoing collaborations with labs in the UK, Germany, Austria, Norway, Russia and other countries. Our main research areas include the ecology of aquatic and soil organisms, microbial ecology and studies of processes in aquatic, wetland and soil ecosystems under anthropogenic stress. We also take part in studies and conservation of some rare and endangered plant and animal species.