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 place in the Czech Republic and is focused on specific regional problems that have been experienced during and after disastrous floods in past 15 years. However, the lessons learned have wider applicability to the issue of flood protection of cultural heritage. Here, we describe two case studies that represent important issues requiring a solution; addressing these issues was the main motivation for the whole project.