Multiple physiological characteristics of the gastrointestinal tract, such as pH, enzymes, illnesses, and microbacteria, influence the stability and absorption of CSNP carriers. The pH of the stomach ranges from 1.5 to 3.5, making it acidic. The pH gradually rises in the small intestine, reaching 5-6 in the duodenum and 7-8 in the jejunum and terminal ileum. Meanwhile, the pH drops to a range of 5.7-6.4 in the caecum before rising again, for the last time, to a range of 6.1-7.5 in the descending colon and rectum. As a result, the medications must be exposed to pH variations along the Gastrointestinal(GI) tract, which may cause drug deactivation, particularly in protein and peptide therapeutics, by modulating differential oxidation, hydrolysis, or deamination. The surrounding pH affects the degree of ionization (pKa) of the drug substrates, hence determining drug solubility and absorption. Chitosan's amino group has a pKa of roughly 6.5, relating to its degree of N-deacetylation, and is completely protonated at a pH of 4, increasing its acidity. As a result, the chitosan-loaded medication exhibits superior mucoadhesive and permeation-enhancing capabilities than the chitosan-free group in the proximal section(the stomach and duodenum), thus improving drug absorption. The problem occurs when chitosan precipitates at pH levels greater than 6.5 in the jejunum, ileum, and colon, thus it has reduced adhesion to the mucus layer of the GI tract, resulting in inefficient medication absorption. To overcome this disadvantage, it is possible to modify chitosan into thiolated chitosan. The distal segment of the GI tract, notably the ileum and colon, is home to the human gut microbiota, which are made up of more than 10 14 microorganisms. The gut microbiota also plays an important role in regulating host metabolism, impacting energy balance, glucose metabolism, and lipid metabolism. The study of medications impacted by gut microbiota gives information on personalized medicine, which predicts drug pharmacokinetics for particular individuals. The human microbiota can influence drug-induced pharmacological and toxicological consequences. For example, the gut flora can change the oral bioavailability and action of insulin since it is vulnerable to proteolysis. CSNPs and its derivatives can regulate gut microbial imbalances. For example, carboxymethyl chitosan has been shown to modify the gut microbiota in Escherichia coli (E. coli)-treated mice, influencing fat and glucose metabolism, as well as the inflammatory profile. Copper-loaded chitosan nanoparticles (CNP-Cu) can enhance the abundance of Bifidobacterium and Lactobacillus, as CNP-Cu inhibits certain bacteria. For instance, Wang et al. investigated the effects of CNP-Cu by feeding it to weaned pigs. The results revealed that the quantity of E. coli was significantly decreased, whereas Lactobacillus and Bifidobacterium populations increased. Several processes, including simple diffusion, active transport, facilitated transport, and pinocytosis, can carry drug molecules past enterocytes and reach the small intestine, which is the primary location for drug absorption. These mechanisms can occur via the paracellular or transcellular route. Drug absorption is significantly hampered by the ATP-binding cassette (ABC) efflux transporters, which have the ability to pump the medications out of enterocytes. P-glycoprotein (P-gp), multidrug resistance protein-2 (MRP-2) and breast cancer resistance protein (BCRP) are among the drug transporter proteins found in the apical side of intestinal epithelial cells. Therefore, nanoparticle carriers like that of chitosan can, in a dose-dependent manner, reduce P-gp expression, as investigated in grass carp, where it increased norfloxacin's oral bioavailability, an antibacterial drug used to treat gram-negative bacterial infections. Commercial chitosan is offered in different grades of deacetylation, molecular weight, and purity. The degree of chitosan purity has a significant impact on the solubility and stability of the material in addition to its biological characteristics, including immunogenicity and biodegradability. High levels of ash and leftover proteins can make it harder for chitosan to dissolve and make it more difficult to construct chitosan-based drug delivery systems. On the other hand, enzymatic hydrolysis of the chitosan may be accelerated by microbiological contamination of the polymer. As a result, the chitosan material needs to be extremely pure and devoid of impurities, including endotoxins when applicable. The relative humidity of the surrounding air has a significant impact on the amount and distribution of moisture in the chitosan substance. Water transport in chitosan material was demonstrated to follow a Fickian process at relatively low humidity levels (below 40%), but an anomalous diffusion kinetic was seen at higher humidity levels. Temperature is another factor that affects the moisture content in chitosan-based systems in addition to relative humidity. It was discovered that exposure to high temperatures (40°C) significantly reduced the moisture content of the chitosan powder (dehydration), which decreased the hardness and mechanical strength of the tablets. Therefore, Maintaining high purity and controlling humidity and temperature are essential for the stability and effectiveness of chitosan-based drug delivery systems.