This study explores the impact of sub-mesoscale structures and vertical advection on the connectivity properties of the Baltic Sea using a Lagrangian approach. High-resolution flow fields from the General Estuarine Transport Model (GETM) were employed to compute Lagrangian trajectories, focusing on the influence of fine-scale structures on connectivity estimates. Six river mouths in the Baltic Sea served as initial positions for numerical particles, and trajectories were generated using flow fields with varying horizontal resolutions: 3D trajectories with 250m resolution as well as 2D trajectories with 250m and 1km resolutions. Several Lagrangian indices, such as mean transit time, arrival depths, and probability density functions of transit times, were analyzed to unravel the complex circulation of the Baltic Sea and highlight the substantial impact of sub-mesoscale structures on numerical trajectories. Results indicate that in 2D simulations, particles exhibit faster movement on the eastern side of the Gotland Basin in high-resolution compared to coarse-resolution simulations. This difference is attributed to the stronger coastal current in high-resolution compared to coarse-resolution simulations. Additionally, the study investigates the influence of vertical advection on numerical particle motion within the Baltic Sea, considering the difference between 3D and 2D trajectories. Findings reveal that denser water in the eastern and south-eastern areas significantly affects particle dispersion in 3D simulations, resulting in increased transit times. Conversely, regions in the North-western part of the basin accelerate particle movement in 3D compared to the 2D simulations. Finally, we calculated the average residence time of numerical particles exiting the Baltic Sea through the Danish strait. Results show an average surface layer residence time of approximately 790 days over an eight-year integration period, highlighting the relatively slow water circulation in the semi-enclosed Baltic Sea basin. This prolonged residence time emphasizes the potential for the accumulation of pollutants. Overall, the study underscores the pivotal role of fine-scale structures in shaping the connectivity of the Baltic Sea, with implications for understanding and managing environmental challenges in this unique marine ecosystem.