The multidrug resistance (MDR) Escherichia coli having Extended-Spectrum Beta-Lactamase (ESBL) genes and the capacity to create a biofilm acts as a major reduction in the therapeutic effectiveness of antimicrobials. In search of a novel nanocarrier (NC) for targeted delivery of antibiotics, carbon dots (CDs) coated calcium carbonate nanocarriers (CCNC) from organic chicken eggshells conjugated with levofloxacin (Lvx) were synthesized. Our main objectives were to explore the antimicrobial, antibiofilm, and NC potential of CDs coated CaCO3 Nanocarrier conjugated with levofloxacin (CD-CCNC-Lvx) to combat biofilm-producing MDR ESBL E. coli of urinary tract infection origin. The synthesized NC system was physiochemically characterized, validating the synthesis of CCNC and CD-CCNC-Lvx with a particle size of 56 and 14 nm, respectively. Scanning electron microscopy (SEM) showed rod shape morphology. X-ray diffraction results discovered crystalline and dispersed nanoparticles. In vitro release drug kinetics illustrated sustained release of Lvx. NC system exhibited strong antibacterial and antibiofilm potential against E. coli with a noticeable low minimal inhibitory concentration (MIC). MIC of CCNC was found to be 30 ± 0.1 μg/mL and CD-CCNC-Lvx was 20 ± 0.1 μg/mL for MDR ESBL-producing E. coli. The synergistic effect of NC upon conjugation with Lvx showed incredible activity with 30 mm zone of inhibition and 68% biofilm inhibition. Flow cytometry analysis revealed treated E. coli cells showed 58.69% reduction in cell viability. SEM images of treated bacterial cells showed morphological changes, which were also confirmed by our flow cytometry findings leading to cell membrane damage in E. coli. NC system also downregulated the blaCTX-M gene in E. coli. The hemolytic analysis proved biocompatibility with human red blood cells (RBCs). It is concluded that CCNC has the potential to be used as NC for target delivery of antibiotics and may combat toxicity of antibiotics as the inhibition of E. coli was noticed at low MIC concentration.