The Mec1/Tel1 kinases (human ATR/ATM) play numerous roles in the DNA replication stress response. Despite the multi-functionality of these kinases, studies of their in vivo action have mostly relied on a few well-established substrates. Here we employed a combined genetic-phosphoproteomic approach to monitor Mec1/Tel1 signaling in a systematic, unbiased, and quantitative manner. Unexpectedly, we find that Mec1 is highly active during normal DNA replication, at levels comparable or higher than Mec1’s activation state induced by replication stress. This “replication-correlated” mode of Mec1 action requires the 9-1-1 clamp and the Dna2 lagging-strand factor and is distinguishable from Mec1’s action in activating the downstream kinase Rad53. We propose that Mec1/ATR performs key functions during ongoing DNA synthesis that are distinct from their canonical checkpoint role during replication stress. Display omitted •A combined genetic-proteomic approach to monitor Mec1 and Tel1 signaling•Mec1 is highly activated during normal DNA replication•Replication-correlated Mec1 action is distinct from canonical checkpoint•9-1-1 clamp and Dna2 lagging-strand factor activate Mec1 during DNA replication Mec1/ATR kinase activity is typically associated with checkpoint signaling in response to replication stress and S-phase DNA damage. Bastos de Oliveira et al. use a quantitative mass spectrometry approach (QMAPS) to demonstrate that Mec1 has “replication-correlated” activity that is distinguishable from its action during canonical checkpoint responses.