Deposition on silica surfaces of two Pseudomonas fluorescens strains (CHA0 and CHA19-WS) having different extracellular polymeric substance (EPS) producing capacities was studied in the absence and presence of cellulose nanocrystals (CNCs). Batch (batch soaking) and continuous flow (quartz crystal microbalance with dissipation) methods were used to evaluate the impact of CNCs on bacterial initial adhesion. This study demonstrated that bacterial initial adhesion to solid surfaces can be significantly hindered by CNCs using both methods. In the presence of CNCs, it was observed that bacteria with more EPS aggregated more significantly compared to bacteria with less EPS, and that bacterial deposition under this condition decreased to a greater extent. The classic DLVO theory failed to predict bacterial adhesion behavior in this study. A detailed discussion is provided regarding potential antibacterial adhesion mechanisms of CNCs.