In recent decades, special attention has been given to the potential association between the gut ecosystem and chronic diseases. Several features and complications of chronic kidney disease (CKD) may induce an unbalanced gut environment, leading to unfavorable consequences for a patient's health. The first section of this review is dedicated to a description of some aspects of gut microbiota and intestinal barrier physiology. The following section explores the impact of CKD on the gut ecosystem and intestinal barrier, particularly the association with uremic toxins, inflammation, and immunodeficiency. Finally, the review describes the state of the art of potential therapies with prebiotics, probiotics, and synbiotics employed to modulate the gut environment and to reduce the generation of colon-derived uremic toxins in CKD.