Water flow induced transport of Pseudomonas fluorescens cells through soil columns was measured as affected by the inoculant treatment. Bacterial cells were introduced into the topsoil of columns, either encapsulated in alginate beads of different types or mixed with bentonite clay in concentrations ranging from 0.5 to 5.0% (w/v). Survival of bacterial cells was improved with the use of alginate or bentonite. Transport, as determined by destructive sampling of the columns, was reduced with the use of alginate encapsulation. Drying of the beads had no influence on transport. The presence of bentonite in the topsoil, either pre-mixed through the soil, or applied as a slurry together with the bacteria, also reduced transport, except when 0.5% was pre-mixed through the soil. P. fluorescens cells encapsulated in alginate beads prepared with water and supplemented with skim milk powder and bentonite showed the best survival during the time of the experiment and the most reduced transport compared to the control. Therefore, cells encapsulated in this way are suitable, due to their optimal survival and reduced spread, for use in a field experiment with genetically manipulated bacteria.