Bacterial transport in unsaturated soils is much less well understood than in saturated conditions, especially for intact soils. This paper aims to investigate the fate and transport of bacteria in intact soils with different water saturations, and particularly the effect of low suction (and hence removal of water flow in the largest macropores). An intact soil column (0.50 m diameter by 0.70 m depth) with a tension infiltrometer was used to investigate the transport and deposition of Bacillus subtilis endospores (i.e. dormant and persistent bacteria) during saturated and unsaturated flows. Soil porosity and pore size distribution were measured. Porosity decreased with depth and macropores were concentrated in the topsoil. Three tensiometers and a temperature sensor were installed along the soil column to monitor matric suction and temperature. Breakthrough curves for bacteria and chemical tracer Br^– at 0 and 0.5 kPa suction were obtained during the 3-month leaching experiment. Bacterial breakthrough occurred earlier than the inert chemical tracer, which is consistent with effects of pore size exclusion. Also, saturated flow gave a significantly higher concentration and recovery ratio of leached bacteria, i.e. 51% v. 0.88%. Recovery of Br^– in leachate at both suctions reached >85%. The column was destructively sampled for deposited endospores at the completion of leaching. Bacterial deposition was concentrated in the top 0.10 m, then decreased abruptly and was relatively constant with column depth, although showing some irregularity at the bottom of the column.