In this study, an attempt has been made to model a real field scenario, whereby an initially almost saturated clay liner in a waste site is gradually drying, due to evaporation at its lower boundary. A detailed conceptual model that deals with the penetration and breakthrough of non-aqueous-phase-liquid (NAPL) in clay liners is introduced. Water content of clay samples was monitored during ambient evaporation through apertures at the base of sample holders. Clay drying rate served as the primary parameter for the NAPL breakthrough study. The interconnection between drying rates, structural damage formation (cracks and suction) and NAPL penetration is especially addressed. The processes taking place in the clay samples during drying appear to be associated with the capillary effects between the different fluid phases in the vicinity of either the NAPL-clay or the clay-air boundaries. A conceptual model of NAPL penetration and breakthrough of the clay layer has been considered, based on both indirect and direct observations of structural damages produced on either clay boundaries. A mutual interaction between these two boundaries is suggested and discussed. NAPL breakthrough is suggested to take place through cracks initiated on the upper soil surface.