Microbial colonisation is important for mineral dissolution in heap bioleaching of low grade ore. Colonisation studies to date have focused on the microbial attachment of single species to mineral concentrates in batch and flow systems. Hydrology and soil engineering studies suggest interaction between microbial colonisation and fluid flow in porous systems that result from solution-ore and microbe-mineral contacting (Wan et al., 1994 and Yarwood et al., 2006).The effect of the irrigation rate on microbial colonisation was assessed using columns packed with acid agglomerated low grade copper-containing ore. Continuous flow, unsaturated, aerated bed reactors were inoculated by pulse irrigation with iron and sulphur oxidising mesophilic microorganisms (1012 cells/ton ore), followed by operation at irrigation rates of 2, 6 and 18 l/m2/h. A novel in-bed sampling technique allowed the extraction of ore samples from the bed during the leaching process. Novel insights regarding microbial growth, interstitial and weakly and strongly attached microbial populations were obtained.Bacterial adherence and cell number retained in the ore bed increased over the 32 day leaching period. Average specific growth rates of ore-associated micro-organisms of 0.161 ± 0.0045, 0.155 ± 0.026 and 0.120 (± 0.00) 1/h were obtained at 2, 6 and 18 L/m2/h respectively. Faster colonisation occurred at lower irrigation rates. At higher irrigation rates, higher detachment and cell removal were apparent, based on PLS cell numbers. The interstitial cells from the stagnant fluid in the ore bed formed the dominant contribution to the microbial population within all the heap systems.