Non-steroidal anti-inflammatory drugs (NSAIDs) are widely recommended for several chronic conditions, including osteoarthritis, rheumatoid arthritis, and cardiovascular disease (CVD). For patients with CVD, low-dose aspirin in particular is recommended as a primary prevention strategy against myocardial infarction. However, long-term intake of NSAIDs can cause damage to the mucosal barrier surrounding the GI tract, leading to the formation of gastric ulcers. While microencapsulation of NSAIDs has been shown to reduce these upper GI effects, sustained release in the lower GI tract and colon may cause epithelial erosion due to increased acidification. In this study, we investigated the role of the NSAIDs aspirin and indomethaci on Na⁺/H⁺ exchanger (NHE) activity in rat colonic crypts. Through comparing rates of pH recovery between control and NSAID perfusion runs, we were able to determine that both aspirin and indomethacin increase hydrogen extrusion into the colonic lumen. Treatment with NHE3 inhibitor 5-ethylisopropyl amiloride (EIPA) and NHE1 inhibitor amiloride further demonstrated that aspirin and indomethacin may preferentially upregulate activity of the apical Na⁺/H⁺ exchanger NHE3. Our results therefore suggest that prolonged clinical exposure to NSAIDs may affect colonic tissue at the site of selected NHE isoforms resulting in modulation of transport and barrier function.