The quantification of microbial colonisation and growth rate kinetics is essential in the characterisation of bioleaching systems for modelling heap performance. An experimental system, designed to simulate heap bioleaching conditions at the agglomerate scale, was used to quantify the microbial growth kinetics of a pure culture of Acidithiobacillus ferrooxidans in the PLS, the interstitial phase and attached to the mineral ore. Conventional methods for the quantification of microbial growth rate kinetics associated with the ore and in the flowing PLS have been found to be inadequate in the characterisation of whole ore systems owing to microbial transport between these regions. Growth within the whole ore system was dominated by the microbial communities associated with the ore. Two models were used to estimate the true growth rate kinetics of Acidithiobacillus ferrooxidans on whole low grade ore as a function of growth and transport between the identified phases. The “hydrodynamics” model assumed that microbial transport was promoted by fluid flow dynamics whilst the “biomass balance” model assumed that the microbial concentration gradient across identified phases was the driving force for transport.