(1) Background: Global agricultural production is projected to increase substantially in the coming decades. Agricultural production provides food and materials crucial to human survival and well-being and is a critical source of livelihood, providing employment opportunities and economic benefits. However, industrialized or intensified agricultural systems, in particular, can have adverse effects on public health, place pressure on natural resources, and reduce environmental sustainability. This review attempts to identify and characterize key environmental health assessment methods for examining a broad array of potential impacts; (2) Methods: Electronic databases Medline, Scopus, Web of Science, and GreenLINE were searched for published literature that presented methods for conducting an environmental health assessment of an agricultural system; (3) Results: Fifty-three sources were included in the review. Eight methods were selected to illustrate the wide range of approaches currently available: health risk assessment methods, health impact assessment, environmental impact assessment methods, environmental burden of disease, lifecycle methods, integrated assessment modeling, trade-off analysis, and economic assessment; (4) Conclusions: This review can provide guidance for selecting an existing method or for designing a new method for assessing the environmental health impacts of an agricultural system.