The Mre11-Rad50-Nbs1 (MRN) heterotrimer plays various and complex roles in DNA damage repair and checkpoint signaling. Its role in activating Ataxia-Telangiectasia Mutated (ATM), the central checkpoint kinase in the metazoan double-strand break response, has been well studied. However, its function in the checkpoint independent of ATM activation, as well as functions that are completely checkpoint independent, are less well understood. In fission yeast, DNA damage checkpoint signaling requires Rad3, the homolog of the ATR (ATM and Rad3-related) kinase, not Tel1, the ATM homolog, allowing us to dissect MRN's ATM-independent S-phase DNA damage checkpoint roles from its role in ATM activation. We find that MRN is involved in Rad3 (ATR)-dependent checkpoint signaling in S phase, but not G2, suggesting that MRN is involved in ATR activation through its role in replication fork metabolism. In addition, we define a role for MRN in the S-phase DNA damage checkpoint-dependent slowing of replication that is independent of its role in checkpoint signaling. Genetic interactions between MRN and Rhp51, the fission yeast Rad51 homolog, lead us to suggest that MRN participates in checkpoint-dependent replication slowing through negative regulation of recombination.