Microwave radiation, a ubiquitous component of modern electromagnetic environments, exerts complex effects on human physiology through thermal and non-thermal mechanisms. This review synthesizes current evidence on its impacts, focusing on the maxillofacial region—particularly salivary glands and the oral microbiome—and systemic effects on immunity and organ systems. Salivary gland responses to microwave exposure are dualistic, with studies reporting altered flow rates, protein secretion, and oxidative stress, linked to ion channel dysfunction, neural-endocrine pathways, or thermal damage. The oral microbiome is disrupted via thermal-induced protein denaturation and non-thermal membrane permeability changes, potentially compromising oral health. Immune modulation by microwaves is context-dependent, ranging from suppressed natural killer cell activity at high intensities to enhanced pro-inflammatory signaling (e.g., NF-κB activation) at low intensities. Systemically, microwave exposure correlates with oxidative stress in the brain, cardiovascular system, and reproductive organs, raising concerns about long-term health risks like cognitive decline and metabolic dysfunction. Despite decades of research, key uncertainties persist regarding low-level chronic exposure, interindividual variability, and cumulative mechanistic interactions. Standardized research and human-relevant models are imperative to refine safety guidelines and mitigate risks in an increasingly wireless society.