In this study, walnut shell (WSh), hazelnut shell (HSh), and mussel shell (MSh) waste as inexpensive reinforcements were recycled for the preparation of epoxy composite materials. Subsequent used inexpensive fillers are chars (WShC and HShC), which are the pyrolysis solid products of the natural WSh and HSh wastes. Three types of epoxy resins: bisphenol-A type (DGEBA), modified with polyurethane (MER with PU), and rubber modified (MER with rubber) epoxy resins were used as the matrix in MSh composites. Thermogravimetric analysis of the composites showed that the thermal strength of the epoxy matrix increased significantly with the MSh and chars. The best water sorption results were obtained with the MSh. The contact angle values of MSh composites prepared with DGEBA epoxy resin were quite high (111°–113.5°) and their water retention values ranged from 0.2% to 0.32%. The composites that were produced using 50 wt% chars and the same epoxy resin showed better flammability stability. The full extinction times were determined as 63 and 58 s for WShC and HShC composites, respectively.