Biodiesel production from rapeseed oil generates various by-products, for example crude glycerol. Glycerol can be utilized by microbial conversion to 1,3-propanediol (1,3-PD), which can be used as a raw material for the synthesis of polyesters and polyurethanes. The results of studies on the synthesis of 1,3-PD from glycerol by use of Citrobacter freundii bacteria were presented. A biosynthesis cost is generally determined based on the costs of nutrients used for culture medium preparation and the costs of broth separation by integrated downstream processes. In this work nanofiltration (NF) was used as a pre-treatment stage for 1,3-PD separation from the broth. Additionally, the NF retentate was reused for the preparation of culture medium, resulting in a change of the initial composition of broth. The catalytic activity of enzymes is strongly affected by broth composition. However, the efficiency of batch fermentations based on the commercial media and NF retentate was similar. Thus, the application of NF process enables a cheaper production of 1,3-PD by biosynthesis. The influence of some broth ingredients, such as carboxylic acids, on variations of biocatalytic properties of used bacteria was discussed. (C) 2016 Elsevier B.V. All rights reserved.