It is now generally accepted that biofouling is inevitable in pressure-driven membrane processes for water purification. A large number of published articles describe the development of novel membranes in an effort to address biofouling in such systems. It is reasonable to assume that such membranes, even those with antimicrobial properties, when applied in industrial-scale systems will experience some degree of biofouling. In such a scenario, an understanding of the fate of planktonic cells, such as those entering with the feed water, has important implications with respect to contact killing particularly for membranes with antimicrobial properties. This study thus sought to investigate the fate of planktonic cells in a model nanofiltration biofouling system. Here, the interaction between auto-fluorescent Pseudomonas putida planktonic cells and 7-day-old Pseudomonas fluorescens resident biofilms was studied under permeate flux conditions in a nanofiltration cross flow system. We demonstrate that biofilm cell recruitment during nanofiltration is affected by distinctive biofilm structural parameters such as biofilm depth.