In recent years, alkali-activated mortar (AAM) has emerged as a promising alternative to ordinary Portland cement (OPC) due to concerns regarding the environmental impact resulting from cement production, which releases carbon dioxide and degrades the quality of the environment. To address these concerns, researchers have explored the addition of supplementary binder materials to enhance cement properties and mitigate pollution. The effectiveness of these binder materials depends heavily on their chemical composition and fineness. Notably, ground granulated blast furnace slag (GGBS) enhances the strength and durability of the cement. In response to the scarcity of river sand (RS), dredged marine sand (DMS) has gained popularity as a potential substitute within the civil engineering field. Furthermore, the integration of nanomaterials has shown promising improvements in the mechanical and microstructural properties of mortar. Therefore, this study aims to investigate the properties of mortar by incorporating nano silica (NS) within the range of 1% to 7%, varying the molarity from 2 M to 8 M, and substituting RS with DMS. The tests carried out encompass a range of evaluations, including compressive strength, flexural strength, SEM-EDS, XRD, UPV, RCPT, and carbonation analysis, to comprehensively assess the properties of the mortar. The study reveals that the AAM demonstrates optimal performance when 50% of RS is replaced by DMS in the absence of NS. Once this optimal point is determined, further analyses are conducted at this value while varying the concentrations of NS from 1–7%. The experimental results indicate that replacing 50% of RS with DMS and incorporating 6% NS leads to maximum compressive strength (49.2 MPa) and flexural strength (9.36 MPa) in the assessed properties. Furthermore, the incorporation of NS in GGBS-based AAM mixes enhances durability by improving resistance against chloride penetration, reducing water absorption, and minimizing carbonation diffusion. Additionally, the microstructural and mineralogical characterization of GGBS-NS-based AAM specimens demonstrates the formation of C-S-H and C-A-S-H gels as the end products of the reactions.