Chondroitin sulfate and sodium alginate were incorporated in different ratios to prepare glutaraldehyde (GA) crosslinked microspheres by water-in-oil emulsion crosslinking method for delivery of 5-flurouracil (5-FU) to colon. Chemical interaction, surface morphology, thermal degradability, crystallinity evaluation, elemental analysis and drug release results were computed by using FTIR, SEM, DSC and TGA, PXRD, EXD and dissolution studies at pH 1.2, pH 6.8 and pH 7.4, respectively. Results revealed an acetal ring formation, non-porous surfaces, stability up to 450 degrees C with mass loss of 84.31%, variation in carbon and oxygen contents and targeted release at pH 7.4. Different kinetic models were applied on release studies i.e., zero order, first order, Higuchi and Korsmeyer-Peppas. Higuchi model was declared as best fit model based on r2 value (0.99) and mechanism of release was non-Fickian diffusion. A potential approach for colonic delivery of 5-FU was successfully developed.