Institute of Aquaculture and Protection of Waters (IAPW) consists of three laboratories and a fish processing unit and shop with fish and aquaculture products located at two sites:

Building ZR Na Sádkách 1780 3D model ZR	Building RH Husova tř. 458/102, České Budějovice 3D model Husova	Processing Unit and Shop with Fish and Aquaculture Products Husova tř. 458/102, České Budějovice e-shop: shop.rybyprozdravi.cz	Aquaponic hall areál kampusu Jihočeské univerzity v Českých Budějovicích, p. č. 1294/15, k. ú. České Budějovice 2 3D model Aquaponic hall

• Laboratory of controlled reproduction and intensive fish culture
• Laboratory of Nutrition
• Processing Unit and Shop with Fish and Aquaculture Products

• Laboratory of Machine Vision in Aquaculture and Water Protection

The Institute of Aquaculture and Protection of Waters primarily engages in research, consulting, educational, and supplementary commercial activities. 

The laboratories in České Budějovice conduct a wide range of research in the areas of pond and intensive aquaculture, fish nutrition, fish immunology, fish ethology, recirculating aquaculture system technology, fish meat processing and quality, open water fisheries, hydrobiology, and water protection. 

The laboratories in Nové Hrady specialize in modern technologies in microscopy, aquaculture, and water protection. They develop data processing methods using statistical and machine learning methods and utilize camera sensors for imaging cells and aquatic organisms. 

The institute thus integrates biological and technological research into a multidisciplinary whole. The institute and its laboratories are involved in the activities of the faculty research center CENAKVA. Through CENAKVA, the institute offers open access to the infrastructure and services of individual laboratories, which are provided free of charge to research organizations. 

Most of the theoretical and practical instruction for the Bachelor's degree programs in Fishery and Protection of Waters and the Master's degree program in Fishery and Protection of Waters takes place in the newly built modern facilities of the IAPW in České Budějovice. Institute staff also supervise doctoral students at the Faculty of Fisheries and Protection of Waters, University of South Bohemia. 

Research and educational activities are supplemented by the commercial activities of the processing unit and shop with fish and aquaculture products – Fish for Health (www.rybyprozdravi.cz). The shop primarily serves to promote and market high-quality fish products. The processing unit and shop with fish and aquaculture products also engage in developing new fish products, practical student training, and preparing buffet menus.