Endoscopy represents a commonly employed technique for canine enteropathies. Different trials in human intestinal endoscopy have suggested that the introduction of water for luminal distension, in place of air, improves the visualization of the mucosal texture and decreases pain. The aim of the study was to compare water immersion (WI) vs. air insufflation (AI) during duodenoscopy in anesthetized dogs in terms of mucosal visualization and nociception. Twenty-five dogs undergoing duodenoscopy were included. The same image of the descending duodenum was recorded applying WI and AI. Each pair of images was analyzed using morphological skeletonization, an image entropy evaluation, and a subjective blind evaluation by three experienced endoscopists. To evaluate differences in nociception related to the procedure applied, heart rate and arterial blood pressure were measured before, during and after WI/AI. To compare the two methods, a t-test for paired data was applied for the image analysis, Fleiss' Kappa evaluation for the subjective evaluation and a Friedman test for anesthetic parameters. No differences were found between WI and AI using morphological skeletonization and entropy. The subjective evaluation identified the WI images as qualitatively better than the AI images, indicating substantial agreement between the operators. No differences in nociception were found. The results of the study pointed out the absence of changes in pain response between WI and AI, likely due to the sufficient control of nociception by the anesthesia. Based on subjective evaluation, but not confirmed by the image analysis, WI provided better image quality than AI.