The reproductive system's chemical and structural integrity is paramount for maintaining reproductive health. Disruptions in species transport and transformation within this system can lead to a plethora of pathophysiological conditions, impacting fertility and pregnancy. These conditions can arise from a myriad of factors including genetic, hormonal, and environmental influences. Understanding the mechanisms of chemical species transport and transformations is essential in elucidating the underpinnings of these conditions and developing effective therapies. This review examines the critical roles of chemical species transport, highlighting the implications for the pathogenesis of common reproductive diseases. It also addresses the interconnectedness between biochemical processes, tissue biomechanics, and the clinical treatment of these conditions.