Stress during development affects maternal behavior and offspring phenotypes. Stress in adolescence is particularly consequential on brain development and maturation, and is implicated in several psychiatric disorders. We previously showed that pre-reproductive stress (PRS) in female adolescent rats affects behavior and corticotropin releasing hormone receptor 1 (CRHR1) expression in first- (F1) and second- (F2) generation offspring. We further showed that offspring phenotypes are partially reversed by post-stress treatment with fluoxetine (FLX) or the CRHR1 antagonist NBI27914 (NBI). Epigenetic processes, such as DNA methylation, are implicated in the stress response and interact with maternal care quality across generations. Here, we asked whether PRS and FLX or NBI exposure would affect maternal care and global DNA methylation in the brains of exposed dams and their adult F1 and paternally-derived F2 offspring. We found that PRS decreased self-care while increasing pup-care behaviors. PRS also increased DNA methylation in the amygdala of dams and their F1 male offspring, but decreased it in F2 females. Drug treatment had no effect on maternal care, but affected DNA methylation patterns in F0 and F1 generations. Furthermore, PRS altered the expression of DNA methylating enzymes in brain, blood and oocytes. Finally, maternal care variables differentially predicted methylation levels in PRS and control offspring. Thus, the effects of adolescent stress are long-lasting and impact methylation levels across three generations. Combined with our findings of epigenetic changes in PRS-exposed oocytes, the present data imply that biological changes and social mechanisms act in concert to influence adult offspring phenotypes.