The decrease of pH level in the water affects animals living in aquatic habitat, such as crustaceans. The molecular mechanisms enabling these animals to survive this environmental stress remain unknown. To understand the modulatory function of neuropeptides in crustaceans when encountering drops in pH level, we developed and implemented a multifaceted mass spectrometric platform to investigate the global neuropeptide changes in response to water acidification in the Atlantic blue crab, Callinectes sapidus. Neural tissues were collected at different incubation periods to monitor dynamic changes of neuropeptides under different stress conditions occurring in the animal. Neuropeptide families were found to exhibit distinct expression patterns in different tissues and even each isoform had its specific response to the stress. Circulating fluid in the crabs (hemolymph) was also analyzed after 2-h exposure to acidification, and together with results from tissue analysis, enabled the discovery of neuropeptides participating in the stress accommodation process as putative hormones. Two novel peptide sequences were detected in the hemolymph that appeared to be involved in the stress-related regulation in the crabs.