The vertical structure of mesoscale eddies in the Lofoten Basin (LB) is investigated by combining satellite altimetry data and the Global Ocean Physics Reanalysis profiles (GLORYS12V1). We apply an automated eddy identification and tracking method to detect and track mesoscale eddies in the LB from altimeter data during the period 1993–2017. The three-dimensional structure of eddies detected is determined from GLORYS12V1 temperature and salinity profiles. A method based on the inferred three-dimensional structure of eddies and eddy trajectories is applied to estimate eddy heat and salt transports in a Lagrangian framework at each point of the track. Note that the study focuses on long-lived eddies (> 35 days) and all analyses are done separately for cyclonic and anticyclonic eddies. Further LB eddies are categorized into four groups based on the locations of eddy generation and dissipation. Our analysis focuses on the region of the quasi-permanent anticyclonic Lofoten Vortex (LV). The maximum in total heat transport associated with LB eddies (anticyclonic, 39.42 × 10¹³ W; cyclonic, 10.56 × 10¹³ W) is observed in the area outside the LV region. On the other hand, while the total salt transport by anticyclonic eddies (27.74 × 10⁵ kg s⁻¹) is also the largest in the area outside the LV region, the maximum total salt transport by cyclonic eddies is found in the LV region (−12.32 × 10⁵ kg s⁻¹). Furthermore, our analysis did not find any significant heat or salt transport into the LV region from the periphery of the Norwegian Current or its immediate neighborhood. The magnitude of heat and salt transports to the LV region from outside is estimated to be 0.9 ×10¹³ W and 1.18 ×10⁵ kg s⁻¹, respectively. Annual averages are 3.6 ×10¹³ W for the heat and 7.2 × 10³ kg s⁻¹ for the salt transport. These numbers estimate the cumulative transfer of heat and salt to the area of the LV from outside that effects on the annual winter regeneration of the LV. KEYWORDS: Lofoten Vortex; Lofoten Basin; Norwegian Sea; mesoscale eddies; altimetry; automatic identification algorithm; heat and salt transports; GLORYS12V1.