This investigation centers on the refined synthesis, characterization, and serum evaluations of orally administered calcium carbonate aragonite nanoparticles (CAN) derived from the shells of the cockle (Anadara granosa). Cockle shells constitute a plentiful and cost-effective source of calcium carbonate, thereby positioning them as a promising candidate for biomaterials in orthopedic and biomedical applications. The synthesis of CAN was accomplished through an optimized protocol including mechanical grinding, purification with lime juice, and regulated precipitation, culminating to the production of highly uniform spherical nanoparticles with dimensions below 50 nm, as corroborated by Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), X-ray Diffraction (XRD), and Energy Dispersive X-ray Spectroscopy (EDX) analyses. The stability and purity of the synthesized nanoparticles were additionally substantiated by thermogravimetric analysis (TGA), which indicated their thermal endurance up to 295°C. In vivo toxicity assessments were performed adhering to OECD protocols (425 and 407 guidelines) utilizing Wistar rats to investigate both acute and sub-chronic toxicological implications across various dosage levels (300, 2000, and 5000 mg/kg for acute studies and 10, 100, and 1000 mg/kg for sub-chronic evaluations). Serum biochemical assays were employed to evaluate hepatic and renal functionalities, oxidative stress indicators, glucose metabolism, and lipid profiles. Findings indicated that while lower concentrations of CAN displayed negligible toxic effects, elevated doses precipitated significant oxidative stress, impairment of liver and kidney functions, as well as modifications in lipid and glucose metabolism, thus suggesting potential nephrotoxicity, hepatocellular injury, and cardiovascular hazards. In conclusion, despite the promising biomedical characteristics of CAN for applications in drug delivery and bone repair, it is imperative that dosage is meticulously regulated to alleviate potential cytotoxic consequences, oxidative stress, and disturbances in metabolic pathways.