Assembly of oppositely charged macromolecules (proteins, DNA, polyelectrolytes) is often used for surface modification and functionalization. Yet, it remains a challenge to control the position and mobility of the molecules within the assembly. Using polyelectrolyte multilayers as model systems, we study the diffusion constant of the polyanion PSS. D-PSS could be varied by 5 orders of magnitude. Two parameters were found to be important: (i) the conformation of the polyelectrolytes and (ii) the molecular weight of the polycation (M-w(PDADMA)); the latter was the dominant parameter. Independent of conformation, by increasing M-w(PDADMA), D-PSS decreased by at least 3 orders of magnitude when M-w(PDADMA) increased by a factor of seven. The decrease was stronger than predicted by any scaling law; it was either exponential or abrupt after D-PSS was almost constant for low M-w(PDADMA). The polymer conformation was adjusted with the salt concentration in the preparation solution. Flatter and less entangled chains led to an increase in D-PSS. These findings on the time dependence of the internal structure of assemblies are discussed in the context of network theory.