Polyelectrolyte multilayers (PEMs) are a versatile category of materials due to their ability to modify surface properties for applications ranging from protective coatings to improved cell adhesion. Polyelectrolyte choice, including its structure and molecular weight (MW), is known to greatly influence PEM assembly and surface properties. In this work, poly(acrylic acid)/poly-l-lysine PEMs using three pairs of MWs (1.8k/15–30k, 100k/120k, and 250k/275k) were studied to determine the effects of their MWs on PEM assembly, topography and surface energy. PEMs assembly was monitored in a quartz crystal microbalance with dissipation, resulting in masses of 3.90 ± 0.87 µg/cm2, 10.80 ± 4.189 µg/cm2, and 30.04 ± 13.68 µg/cm2 for 10 bilayers of low, medium, and high MW pairs, respectively. The low MW PEM was more rigid. Low and high MW PEMs exhibited higher roughness than medium MW, caused by polyelectrolyte stripping. Surface energy remained constant with bilayer count in the low and high MW PEMs, but steadily increased in the medium MW PEM. Differences between medium MW PEMs from low and high MW systems indicate that, while PEM properties change with MW, they are not monotonically correlated and are instead related to changes in internal charge distributions and the resultant stripping that may occur.