Watermarks are the most important tool for dating undated documents written on paper. Hence, catalogues and databases of watermarks play an eminent role for the work of medievalist and paper historians. This article presents an overview of an integrated software system developed for storage, retrieval, manipulation, digital processing, and identification of watermarks in old manuscripts. The full processing pipeline from the scanning to the identification of watermarks is described. The main part of these watermarks was captured from manuscripts stored in the Klosterneuburg monastery (Austria).