Abstract: Natural porous media such as soils or aquifers are characterized by various pore-scale heterogeneities. This includes the temporal variability of substrate supply and the spatial heterogeneity of pore sizes. As a consequence, microbial growth conditions in natural porous medium environments may differ from typical laboratory setups used to study microbial behavior. Pore-size heterogeneities and the resulting transport regime can lead to highly complex distribution patterns of substrates and corresponding microbial growth conditions including the frequent occurrence of stress periods for the microbial population. Microorganisms can respond to such stress periods by switching from an active into an inactive or dormant state, and the corresponding microbial abundance and dynamics may exhibit rather complex temporal and spatial patterns. This study applies an extended modeling concept for the growth and degradation activity of microbial species able to switch between two different physiological states. The concept is implemented into a pore network model that allows simulating the changes in microbial growth conditions in heterogeneous porous media. The model is used to study the impact of pore-size heterogeneities on the distribution and activity of a bacterial community consisting of two competing species. Simulation results show that such pore-scale heterogeneity has a strong impact on bacterial abundance and activity, creating a complex structure of microbial niches. This leads to an increased coexistence of microbial species at both the microscale and the macroscale, although in the macroscale, the total biomass concentration is less affected by these heterogeneities.