Carriers with a germline mutation in the BRCA1 gene have an increased lifetime risk of breast and ovarian cancer and other malignancies. Cancer initiation is linked to mutagenesis and loss of heterozygosity (LOH) in BRCA1 carriers. Approximately 70% of BRCA1-associated breast cancers are triple negative (TNBC; progesterone (PR), HER2, estrogen receptor (ER)-negative), which were reported to develop from ER/PR-negative luminal progenitor cells. However, the mechanisms and factors inducing carcinogenesis in ER/PR-negative cells carrying a BRCA1 germline mutation are not known. Also, ER/PR-negative breast cancer cells are not responsive to ER hormone therapy, making it challenging to treat TNBC cancers. We investigated ER-negative mammary cells and found that estrogen and estrogen metabolites, which are known to form DNA adducts, inhibit replication fork progression in heterozygous BRCA1mut/+ mammary cells. Furthermore, estrogen triggered DNA breaks, large deletions, and cancer-initiating mutations, such as LOH in BRCA1mut/+ mammary cells. In addition, we found that one of the most commonly used herbicides in the US, the endocrine-disruptor Atrazine, also hinders replication fork progression and induces genomic instability in these cells. To counteract the genotoxic effect, we tested several dietary compounds and found that Indole-3 carbinol (I3C) prevents the replication stress and reduces genomic instability in BRCA1mut/+ mammary cells. In summary, these results reveal that alterations in estrogen metabolism caused by environmental or endogenous factors are genotoxic for ER-negative BRCA1mut/+ mammary cells. And our results also show that the dietary compound I3C can prevent estrogen-induced DNA damage, and suggest that I3C can be a potential cancer-preventive therapeutic agent for BRCA1 carriers.