For nano-scale surface modification and biofabrication purposes, it is necessary to first understand the variations in adsorption behavior of certain carbopolymers. Assembled polyelectrolyte multi-layers (PEMs) composed of two naturally-derived polyelectrolytes; chitosan (CHI) and alginate (ALG) were alternatively deposited via the layer-by-layer technique-in reversed order-on planar gold (Au) surfaces and monitored in situ by means of quartz crystal microbalance with dissipation (QCM-D) in real-time. QCM-D revealed that [ALG-CHI]10 flilms were compact yet soft with thickness in the range of 240 nm compared to a more open [CHI-ALG]10 system with 91 nm. Such differences in visco-elastic properties of PEMs were the result of different growth regimes employed. To the best of our knowledge, this is the first QCM-D demonstration of the difference in multi-layer structure by alternate assembly of ALG and CHI on a flat surface. Findings suggest that more robust PEMs could be produced when ALG is the prime base layer.