Ongoing thought patterns constitute important aspects of both healthy and abnormal human cognition. However, the neural mechanisms behind these daily experiences and their contribution to well-being remain a matter of debate. Here, using resting-state fMRI and retrospective thought sampling in a large neurotypical cohort ( n = 211), we identified two distinct patterns of thought, broadly describing the participants’ current concerns and future plans, that significantly explained variability in the individual functional connectomes. Consistent with the view that ongoing thoughts are an emergent property of multiple neural systems, network-based analysis highlighted the central importance of both unimodal and transmodal cortices in the generation of these experiences. Importantly, while state-dependent current concerns predicted better psychological health, mediating the effect of functional connectomes, trait-level future plans were related to better social health, yet with no mediatory influence. Collectively, we show that ongoing thoughts can influence the link between brain physiology and well-being. Author Summary Occupying a considerable portion of our waking lives, spontaneous thoughts constitute the foundations of our rich inner mental experiences and well-being. Nevertheless, the neural mechanisms behind this cognitive process and its relation to our mental health remain unresolved. In a large cohort of participants, we show that distinct dimensions of ongoing thoughts emerge from a broad set of whole-brain functional interactions, with certain patterns significantly mediating the link between brain connectivity and psychosocial health. Overall, these results highlight the heterogeneous nature of self-generated thoughts, the content and form of which have a significant influence on the association between our brain physiology and mental well-being.