The transport of a genetically modified strain of Pseudomonas fluorescens, BR12, and its parent, BR5, was studied after irrigation of undisturbed clayey and sandy soil cores, simulating heavy tropical rainfall (56.6 mm/h). Vertical transport of both inoculant strains was detected in all soil cores. Transport was negatively affected by the organic matter content of soil, whereas soil texture did not affect the degree of transport. Both factors influenced the survival of the introduced bacteria, in particular that of the modified strain. The initial moisture and structural status of the clayey soil, which was related to seasonal influences, also influenced the degree of bacterial translocation. In cores with two clay soil types, the genetically modified strain was transported to a greater extent than its parent. However, the modified strain showed similar or lower survival rates than its parent in topsoil layers of the different clay soil type and the sandy soil cores. Counts of culturable cells of both inoculant strains in the percolation water remained roughly stable or decreased during the experiment, and the inoculant survival was clearly affected by the soil from which the percolation water was obtained. Both strains showed good survival in the percolation water from microcosms-containing clay soil enriched with manure to about 6% organic matter, whereas their population sizes declined in percolation water from non-manured clay or sandy soil cores. The results suggested that the release of derivatives of P. fluorescens strain BR5 into soils in tropical climates should be carefully planned and monitored in order to guarantee their efficacy as biocontrol agents and to assess the potential contamination of ground and surface waters.