The theme of this special issue is to explore the new territories beyond conventional subsurface flow and transport theories. We have selected 12 articles in this special issue and these articles cover a wide range of problems including (1) Non-Fickian chemical transport in various environments; (2) Non-Darcian flow; (3) Flow and transport in low-permeability media; (4) Vadose zone process; (5) Regional scale groundwater flow and groundwater-surface interaction; (6) Innovative numerical methods. The major contributions of these papers are summarized in this editorial.