The gastrointestinal (GI) system plays a crucial role in maintaining homeostasis by facilitating nutrient absorption, eliminating waste, and protecting against pathogenic microorganisms. Understanding the pathophysiological conditions of the GI system necessitates a deep comprehension of how chemical species transport and transformation contribute to disease states. This review focuses on the mechanisms by which these processes impact the pathogenesis and progression of gastrointestinal diseases, particularly gastroesophageal reflux disease (GERD).