We here describe the July 2011 flooding of the Danish Diet, Cancer and Health biobank, which contained blood and urine samples and fat tissue biopsies from 57,053 Danes. We use this as a starting point to detail empirically derived knowledge on how to best restore and secure a biobank and test the quality of flooded samples; a process which has taken place over the subsequent 2-year period. The aim is to generate a framework for such a restoration process, which may be useful in relation to future biobank floods. The framework includes four steps: 1) freeze-drying of the samples, 2) cleaning and reorganization of the samples, 3) quality testing of the samples, and 4) documentation and communication. Furthermore, we present general experiences derived with regard to planning, financing, and stakeholder contact in such a restoration process.