Accumulating data suggest that various forms of meditation are beneficial for both mental and physical health. However, the neural mechanisms underlying these effects remain unknown. This study directly examines the fluctuating and dynamic aspects of mental processing during meditation using a novel subject-determined fMRI design. To accomplish this, we put forth a model of naturalistic cognitive fluctuations between mind wandering and attentional states that occur during the practice of focused attention meditation. This model specifies four intervals in a cognitive cycle: mind wandering, awareness of mind wandering, shifting of attention, and sustained attention. Using subjective input from experienced meditation practitioners indicating the moment of awareness of mind wandering, we found that these four cognitive phases were associated with activity in different brain networks. Specifically, we identified activity in default mode regions during mind wandering, and in salience network regions during awareness of mind wandering. Elements of the executive network were active during shifting and sustained attention. Furthermore, resting state functional connectivity of these networks was dependent on lifetime meditation experience. Understanding the neural changes that occur with meditation will improve our ability to apply contemplative practices more effectively, with the goal of increasing well-being for healthy and disease populations.