The macromolecular organization in system composed of anionic poly(acrylic acid) (FAA) and cationic chitosan (Cs), with different degrees of deacetylation (DD), under extensive elongational flow, is described. Cs/PAA nanofibers were obtained, and polyelectrolyte complexation only occurred when fibers were immersed in fluid media of a certain pH. Assembled polyelectrolytes complexes formed a pH-triggered system, as demonstrated by reversible change of the swelling degree, by 3 orders of magnitude, and a change on the elastic modulus, by 2 orders of magnitude. Both the swelling degree and the elastic modulus proved sensitive to the DD of Cs. Rheological measurements showed that increased DD of Cs resulted in a decrease in viscosity of both pure Cs and precursor Cs/PAA solutions, attributed to repulsive interactions between ionized amino groups in Cs. At the same time, a DD-dependent change in balance between hydrogen bonding and ion-dipole interactions between the components in Cs/PAA, was responsible for the more pronounced viscosity decrease in these solutions.