In order to study the mechanical and microstructural properties of masonry mortar, combined particles of cockle and scallop seashell wastes were incorporated and analysed through destructive and non-destructive tests. River sand was replaced with the combined seashell particles (SPs) at seven mixes, viz., 0, 5, 10, 15, 20, 25, and 30% with a 0.5 constant water-to-cement ratio (W/C). A mortar mix design of M4-type of BS EN 1996-1-1 was adopted with a target compressive strength of 5.17 MPa at 28 days. The physical, chemical and mineralogy properties of the SPs were analysed through BS standard sieving, X-ray fluorescence (XRF), scanning electron microscopy (SEM), and X-ray diffraction (XRD) methods. The hardened SP-based mortars were subjected to direct compressive strength, rebound hammer, ultrasonic pulse velocity tests, and nonevaporable degree of hydration analysis. The XRF, SEM, and XRD analysis results of the SPs showed over 86% calcium oxide content, irregular and needle-like particles, and hydroxyapatite/calcium silicates, respectively. The direct compressive strength and the non-destructive test results revealed that up to 30% sand replacement with SP in masonry mortar, an improvement of 45% compressive strength could be attained over the control sample. The nonevaporable water method of the degree of hydration analysis showed that after 28 days, hydration increased considerably for the SP-blended mortars over the control, especially the SPM-30 with 30% sand replacement. Therefore, the study concludes that the investigated SPs in blended masonry mortar could benefit an eco-friendly environment and conservation of natural resources.