Wastewater monitoring is highly efficient in SARS-CoV-2 surveillance for tracking virus spread through travel, surpassing traditional airport passenger testing. This study explored the links between SARS-CoV-2 contents and variants from aircraft to city, assessing the impact of detected variants from international travellers versus the local population. A total of 969 variants using next-generation sequencing (NGS) were examined to understand the links between—aircraft, Arlanda airport, wastewater treatment plants (WWTPs), and Stockholm city—and compared these to variants detected in Stockholm hospitals from January to May 2023. SARS-CoV-2 contents in WWTPs reflected local infection rates, requiring analysis from multiple plants for an accurate city-wide infection assessment. Variants initially detected in aircraft arriving from China did not spread widely during the study period. RT-qPCR is adequate for the detection of specific variants in wastewater, including Variants Under Monitoring. However, NGS remains a powerful method for identifying novel variants. Wastewater monitoring was more effective than clinical testing in the early detection of specific variants, with notable delays observed in clinical surveillance. Furthermore, a broad range of variants are detected in wastewater that surpasses clinical tests. This underscores the vital role of wastewater-based epidemiology in managing future outbreaks and enhancing global health security.