This contribution discusses some results of the ongoing research focused on the protection of cultural heritage from flood danger. The research project Methodology of Protection and Rescue of Cultural Heritage against Flood takes part in Czech Republic and is focused on specific regional problems that have been experienced during and after disastrous floods in the past 15 years. The author would like to show that rivers should be seen not only as a threat but also as a very important space-creating element, life source, connection and border between places. There is great need of an interdisciplinary approach in planning of flood protection systems where not only a technical but also an architectural, cultural, esthetical and historical point of view would be taken into account. The author has to have in mind that each field of knowledge has only a limited point of view but urban areas especially with cultural heritage on site are very complex systems that require also a complex approach to solve the flood problem. Otherwise, as the author experienced in many case studies, there could be more harm done by a flood protection system than by the flood itself. When a river is cut off from the city it can create a very unnatural environment that ends up in dead places and the decomposition of the former urban structure.