Unstable biopolymer solutions inevitably lead to mis-characterization of macromolecular properties and irreproducible results. Even under stable or quasi-stable conditions, persistent aggregates can hamper reliable characterization, especially using light scattering methods. Various pitfalls in characterizing biopolymers were worked through, including determination of solution stability zones, dissolution kinetics, estimation of fraction of aggregate populations, and the relationship between batch and fractionation methods. Chitosans, polyampholytic biopolymers with isoelectric point around pH = 6.0, with varying degrees of carboxymethylation were studied. Instability was determined vs. pH and ionic strength using a high throughput screening method, simultaneous multiple sample light scattering (SMSLS). With stable solution conditions determined, equilibrium batch and multi-detector GPC characterization of molecular weight, intrinsic viscosity, and polyelectrolyte properties was made. Finally, a first attempt at continuous online monitoring of the modification reaction itself was made and compared to FTIR analysis of carboxymethylation on discrete aliquots. Given the range of possible characterization problems, multiple approaches with independent instruments may be required for reliable natural product characterization. Online monitoring of modification reactions may lead to rapid advances in understanding and preparation of natural products.