After successfully completing his/her studies the graduate is able to:

• explain basic processes and system function in different types of aquatic ecosystems;
• determine water invertebrates of central European water ecosystems
• have basic knowledge of biotechnology of wastewater plants and drinking water works
• explain impact of regulations, pollutions and other anthropogenic influences on water ecosystems
• know the use of topical bioindication methods and statistical evaluations in the R-System

Graduates are fully schooled in the problems of ecology of running waters, with basic knowledge of the ecology of standing waters, ecotoxicology of the water environment, production ecology, and related fields. They are specialists in certain taxonomic groups, with expanded knowledge of taxonomy, and identification and biology of water invertebrates and vertebrates. Graduates find employment as specialists and researchers at research institutions of the Ministry of the Environment, the Academy of Sciences of the Czech Republic, and universities. In view of the fact that the graduates are well-informed about all trends in research on flowing waters, their knowledge is comparable to graduates of e.g. Vienna University or other European universities. Therefore, they are highly employable abroad.

The standard duration of doctoral study programme is 8 semesters

In the doctoral degree programme the supervisor together with the doctoral candidate prepare a general four-year plan and a detailed study plan for the first year. The general plan is an outline of stages and contains transparent time frames for field or laboratory work aimed at data gathering and processing, evaluation and writing the dissertation. The plan also contains a date for taking the test in English (if the applicant cannot show an appropriate certificate at the PhD interview), and usually an internship at domestic and foreign departments, or independent participation at academic conferences, seminars or workshops. A detailed study plan for the 1st year includes the required lectures for all doctoral students. It also contains active participation in seminars and in teaching (max. 2 hours a week). The study plan for the next two years covers required attendance at seminars and individual lectures (min. 6 – 8 lectures, mostly within the first two years) and independent background reading in the research area according to the schedule or upon agreement with the supervisor.

At the conclusion of their studies, doctoral candidates must take the state exam. The exam is taken orally before a committee of specialists and the assessed areas include the candidates' field of research and fields related to their research. The oral exam deals with ecology of flowing waters with focus on communities in terms of structure, interrelationships, and bio-production. Questions from related fields usually regard hydraulic and hydrological parameters, individual substance cycles, bioaccumulation of contaminating substances, etc. By the time the state exam is taken, the doctoral students must demonstrate proof of their proficiency in English: give an academic lecture at a conference abroad (including poster presentations if the conference organizes poster presentation competition) or write a commentary with discussion in English. It is also required that before taking the state exam at least two articles are published in ISI journals; at least one of them should deal with the topic of the dissertation (preliminary results) and the student should be the first author. t is strongly recommended min. 3 Monthly stay abroad for dissertation topic.

The dissertation must present completely new and original results of the research problem, or it can consist of several already published articles accompanied with the doctoral student's commentary (at least two articles published in impact journals or in press). The dissertation may be written in Czech with a summary in English. If a foreign opponent is chosen, the paper must be translated into English. An extensive summary of results written in English is an integral part of the state exam documentation. The summary also contains a list of the doctoral candidate’s previous publications.