Disinfection byproduct (DBP) exposure has been linked to multiple adverse health outcomes. However, the molecular initiating events by which DBPs induce their toxicities remain unclear. Herein, we combined reporter cell lines and activity-based protein profiling (ABPP) chemical proteomics to identify the protein targets of three monohaloacetic acids (mHAAs) and three monohaloacetamides (mHAMs), at the proteome-wide level. While mHAAs and mHAMs have similar potencies in reducing MTT activity, mHAMs induced greater Nrf2-mediated oxidative stress responses, demonstrating their distinct toxicity pathways. ABPP on crude cell lysates suggested that general proteome thiol reactivity correlates with cytotoxicity. Interestingly, live cell ABPP results revealed class-specific proteins attacked by mHAMs or mHAAs. Subsequent proteomic analysis identified >100 unique targets per DBP. mHAMs preferentially react with redox proteins including disulfide oxidoreductase enzymes, accounting for their stronger Nrf2 responses. To further probe alkylation mechanisms, we directly monitored protein adducts and identified 120 and 37 unique peptides with iodoacetamide and iodoacetic acid adducts, respectively. Of the latter, we confirmed glyceraldehyde-3-phosphate dehydrogenase as a key target of IAA, specifically attacking the catalytic Cys 152. This is the first study reporting the distinct cellular protein targets of mHAAs and mHAMs at the proteome-wide level, which highlights their different toxicity pathways despite their similar structures.