The combination of Layer-by-Layer (LbL) self-assembly of oppositely charged polymers with the concept of molecular imprinting in polymers promises faster loading/unloading as compared to bulk systems. Here, we monitor the construction of LbL self-assembled polyelectrolyte multilayers (PEM) including template molecules and the binding and release dynamics of the guest molecules in the imprinted sites employing a quartz crystal microbalance with dissipation measurement (QCM-D). It is found that pH-dependent removal and rebinding of the template leads to a simultaneous swelling of the film. Separating the swelling from the template kinetics is a task which can be carried out by careful interpretation of the obtained QCM-D data. Considering correlated frequency and dissipation changes, evidence is found that the film features binding sites that can be loaded with the template such that the major part of template uptake is due to selective binding into imprinted sites. Template uptake is causing an enhanced cross-linking, as monitored by a reduced dissipation. The mechanism of reversible template uptake and release is shown to be based on the charge equilibrium in the film, which is manipulated by pH variation.