Peptides are essential components of all living organisms, widely present in the environment, and play important roles in diverse environmental processes. Some peptides are a cause of concern for ecosystems and for environmental health, including drinking water safety. Peptides may impact the environment through their involvement in nitrogen cycles, cloud formation, and many other biogeochemistry processes. Some environmental peptides (e.g. microcystins, MCs) originating from microorganisms are highly toxic, and thus their distribution and transformation in the environment are of great health concern. Many analytical tools have been developed to characterize environmental peptides. The analysis of peptides in environmental samples is challenging, however, owing to their high chemical and structural diversities, low abundance, and complex sample matrices. Mass spectrometry (MS) has become one of the most attractive techniques for environmental peptide analysis, because of its high sensitivity and selectivity. In this article, we summarize the recent advances in MS methods for the analysis of peptides in environmental samples. Particularly, we discuss the analytical developments for the analysis of peptides in water, atmospheric aerosols, and soils, as each sample type represents a distinct analytical challenge.