Pore network models (PNMs) offer a computationally efficient way to analyse transport in porous media. Their effectiveness depends on how well they represent the topology and geometry of real pore systems, for example as imaged by X-ray CT. The performance of two popular algorithms, maximum ball and watershed, is evaluated for three porous systems: an idealised medium with known pore throat properties and two rocks with different morphogenesis—carbonate and sandstone. It is demonstrated that while the extracted PNM simulates simple flow (permeability) with acceptable accuracy, their topological and geometric properties are significantly different. This suggests that such PNM may not serve more complex studies, such as reactive/convective transport of contaminants or bacteria, and further research is necessary to improve the interpretation of real pore spaces with networks. Linear topology–geometry relations are derived and presented to stimulate development of more realistic PNM.