The goal of this work is to explore the effects of solution ionic strength and pH on polyelectrolyte multilayer (PEM) assembly, using biologically derived polysaccharides as the polyelectrolytes. We used the layer-by-layer (LBL) technique to assemble PEM of the polysaccharides heparin (a strong polyanion) and chitosan (a weak polycation) and characterized the sensitivity of the PEM composition and layer thickness to changes in processing parameters. Fourier-transform surface plasmon resonance (FT-SPR) and spectroscopic ellipsometry provided in situ and ex situ measurements of the PEM thickness, respectively. Vibrational spectroscopy and X-ray photoelectron spectroscopy (XPS) provided details of the chemistry (i.e., composition, electrostatic interactions) of the PEM. We found that when PEM were assembled from 0.2 M buffer, the PEM thickness could be increased from less than 2 nm per bilayer to greater than 4 nm per bilayer by changing the solution pH; higher and lower ionic strength buffer solutions resulted in narrower ranges of accessible thickness. Molar composition of the PEM was not very sensitive to solution pH or ionic strength, but pH did affect the interactions between the sulfonates in heparin and amines in chitosan when PEM were assembled from 0.2 M buffer. Changes in the PEM thickness with pH and ionic strength can be interpreted through descriptions of the charge density and conformation of the polyelectrolyte chains in solution.