This study investigates the effects of different waste shells on the material characteristics and properties of cement-based composites. The accumulation of large quantities of waste shells poses significant environmental concerns, leading to soil pollution and odors. Furthermore, the construction industry contributes to global environmental issues through high energy consumption and CO${}_2$ emissions during aggregate production. Recycling different waste shells, including cockles, oysters, and murex, after cleaning them using an ultrasonic device, and incorporating them as partial substitutes for fine aggregates, can potentially tackle both environmental challenges. The physical and mechanical properties, including freeze–thaw resistance, of mortar specimens with different types and amounts of waste shell aggregates were measured, to examine the effect of each shell aggregate on the specimens. The microstructural characteristics of the specimens were investigated using X-ray diffraction (XRD), scanning electron microscopy (SEM), and micro-computed tomography (micro-CT) and correlated with the material properties. The results demonstrate that mortars incorporating waste shells, with appropriate treatments such as 30% replacement and washing of the particles, exhibit compressive strength up to 90% of that observed in the normal case. Therefore, these shells can be effectively used as substitutes for fine aggregates.