The potential for nanofiltration (NF) in removing both relatively low molecular weight (MW) organic species and charged solutes from complex media is noteworthy. The main aim of the current work was to improve understanding of the separation mechanisms of fermentation broths components in the NF process. For this purpose, the experimental investigations were performed using the commercial polyamide NF270 membrane. The feed solution was ultrafiltered 1,3-propanediol (1,3-PD) broths. The separation results were analyzed and discussed in light of the detailed characteristics of both the membrane and the broth components. It has been noted that the membrane ensured the complete 1,3-PD permeability and significant rejection of some feed components. A thorough analysis showed that the retention of carboxylic acids was based on both the Donnan effect and sieve mechanism, according to the following order: succinic acid > lactic acid > acetic acid > formic acid. Indeed, acids retention increased with increasing charged acids ions valency, Stokes radius (rS) as well as MW, and decreasing diffusion coefficient (D). In turn, for ions, the following orders retention was determined: SO42− = PO43− > Cl− and Ca2+ > Na+ > NH4+ ~ K+. It indicated that the ions retention increased with increasing ions charge density, hydrated radius (rH), and hydration energy (Eh). It showed that the separation of the ions was based on the Donnan exclusion, sieving effect, and dielectric exclusion.