Two different fucoidan polymers (unfractionated Fucus vesiculosus fucoidan, and fractionated low molecular weight Fucus vesiculosus fucoidan) have been used to create substrates for protein adsorption studies. Polyelectrolyte multilayers were formed using the fucoidans (polyanions) with chitosan as the corresponding polycation. Multilayer formation was studied using zeta potential measurements, quartz crystal microbalance with dissipation monitoring (QCM-D) and attenuated total reflectance (ATR) FTIR spectroscopy. The formation studies reveal that the low molecular weight (LMW) fucoidan produces a less hydrated multilayer, with a significantly increased adsorbed mass, and with fucoidan as the diffusing species during formation. Protein adsorption studies using bovine serum albumin (BSA) were undertaken for solution conditions designed to mimic biological conditions, and to minimise the role of electrical double layer forces in influencing adsorption. Under these conditions, and as revealed by ATR FTIR spectroscopy, BSA is seen to adsorb less substantially to multilayers formed with the LMW fucoidan, and to cause extraction/stripping of the LMW fucoidan from the multilayer. FTIR spectra reveal that the protein adopts a different conformation when adsorbed to the LMW fucoidan multilayer, both relative to the protein in solution and when adsorbed at the surface of the multilayer formed from unfractionated fucoidan.