Information on pathways leading via voids in biomolecules and their use for ligand transport is critical to understand the function of many biomolecules. The TransportTools library was developed to facilitate investigation of the pathways and their utilization in large, simulated datasets with a ready-to-use workflow, and provide an environment to develop new custom-made tools. TransportTools is implemented as Python3 module and distributed as pip and conda packages. The source code and the user guide are available here.