A new all-aqueous process is described to form three-dimensional porous silk fibroin matrices with control of structural and morphological features. The result of this process are scaffolds with controllable porosity and pore sizes that fully degrade in the presence of proteases, unlike prior methods to generate silk-based biomaterials that required the use of organic solvent treatments to impart control of structure and stability in aqueous environments, with low rates of proteolytic hydrolysis. A mechanism is proposed for this novel process that imparts physical stability via hydrophobic interactions. Adjusting the concentration of silk fibroin in water, and the particle size of granular NaCl used in the process, leads to the control of morphological and functional properties of the scaffolds. The aqueous-derived scaffolds had highly homogeneous and interconnected pores with pore sizes ranging from 470 to 940 microm, depending on the mode of preparation. The scaffolds had porosities >90% and compressive strength and modulus up to 320 +/- 10 and 3330 +/- 500 KPa, respectively, when formed from 10% aqueous solutions of fibroin. The scaffolds fully degraded upon exposure to protease during 21 days, unlike the scaffolds prepared from organic solvent processing. These new silk-based three-dimensional matrices provide useful properties as biomaterial matrices due to the all-aqueous mode of preparation, control of pore size, connectivity of pores, degradability and useful mechanical features. Importantly, this process offers an entirely new window of materials properties when compared with traditional silk fibroin-based materials.