Improved methods for the separation and isolation of bioactive polyelectrolytes, such as humic acid, fulvic acid, ulmic acid, and humin, from any one or a combination of naturally occurring or synthetically produced humified organic matter (HOM) are described. The methods involve the application of an electromagnetic field to an aqueous slurry of the HOM to thereby separate one or more bioactive polyelectrolyte fractions from the remaining of the HOM. Related systems and isolated bioactive polyelectrolyte fractions are also described.