Layer-by-layer (LbL) assemblies have remarkable potential as advanced functional materials with applications in energy and biomedical related areas. However, very little is known about their thermal and viscoelastic properties owing to the inherent difficulty in their accurate measurement Here we report on the thermal behavior of a model LbL system containing weak polyelectrolytes poly(allylamine hydrochloride) (PAR) and poly(acrylic acid) (PAA) as a function of assembly solution pH. Quartz crystal microbalance with dissipation (QCM-D) and modulated differential scanning calorimetry (DSC) indicate that hydrated PAH/PAA LbL assemblies undergo a thermal transition that is akin to a glass transition for most assembly pH's investigated, with the exception being the case where both polyelectrolytes are fully charged. The nonmonotonic dependence of the glass transition temperature of the PAH/PAA LbL system with respect to assembly pH is discussed in relation to the film's hydration, composition, film growth mechanism (linear vs exponential), and ion pairing density.