The gastrointestinal (GI) tract actively transports food along different organs to mix it with secretions and break down food particles, which can then be absorbed by the body while waste is eliminated. This involves a variety of biological, chemical, and physical phenomena. Understanding flow phenomena in the GI tract is important for human health, as it can impact drug delivery, the spatiotemporal organization of the microbiota, and lead to health problems related to GI motility dysfunction. This presentation demonstrates how the gastrointestinal tract handles complex flow by providing two examples: one at the organ scale and the other at the microscopic scale. The first example aims to demonstrate how complex fluid dynamics modelling of video defecography can aid in diagnosing defecation disorders. A two-dimensional patient-specific simulation was developed based on standard X-ray video defecographies to quantify velocity, pressure, and stress fields during defecation for patients with normal and pathological defecatory function. The results showed that normal defecation involved a proximal–distal pressure gradient from both the anorectal junction and the anal canal, with the flow dominated by shear-thinning viscous properties. Impaired defecations were also simulated and compared to normal defecation, leading to a discussion of critical factors that could aid in effective medical management. In the second example, the focus is on how fluid is transported and mixed at small scales using microscopic finger-like structures, the so-called villi. A numerical model was developed to simulate flow and mixing due to the active movement of villi. By using the physiological pattern of contractions, it was shown that villi can either transport fluid in the longitudinal direction of the small intestine and/or induce radial mixing. These phenomena are due to a combination of geometric effects (wave propagation) and inertia at moderate Reynolds number.