Stable, responsive and autofluorescent genipin-crosslinked chitosan–poly(vinyl pyrrolidone) hydrogels have been synthesized. Morphological characterization techniques such as scanning electron microscopy, environmental scanning electron microscopy, and in situ confocal laser scanning microscopy (CLSM), in both reflectance and fluorescence modes, have been compared for their suitability to characterize the network structure of these hydrogels. CLSM is shown to be the optimal technique owing to the facile generation of the three-dimensional porous architecture and extra topographical information while the sample is immersed in the aqueous solution to which it will find application. CLSM is used in both reflectance and fluorescence modes to follow morphology variation as a function of time during swelling. Conveniently, acquisition via reflectance produces images with a higher degree of structural detail than fluorescence, widening the application of this method to characterize hydrogels where addition of a fluorescent probe, which may alter the native structure, is undesired.