The spatial and temporal variations of Lagrangian Coherent Structures (LCSs) in the Baltic Sea are extracted from finite-time Lyapunov exponent (FTLE) fields. A validated 3-D hydrodynamic model of the Baltic Sea coupled with a water quality model is applied for the years 2000-2009. The novelty of the work is on the variation of LCSs with the sea depth, the state of hypoxia and the possible relationship with the blooming patterns in the Baltic. The study reveals a variety of LCSs with a typical core diameter of 10-40 km and a duration of 2-7 days that are formed offshore in all the basins of the Baltic Sea. They occur throughout the year even during winter times when the sea at the northern basins is partially covered with ice. The LCSs are more abundant in the southern basins where extensive algae blooms occur. The dominant structures are large vortex dipoles and anti-rotating vortex pairs that are not limited to the surface water layer but spread to a depth of 143.5 m. Likely mechanisms for the formation and the spread of LCSs are Kelvin-Helmholtz type instabilities, Proudman-Taylor column and Ekman Spiral. In the vicinity of the shorelines, the LCSs are smaller in diameter scaling with the mean Rossby radius to around 5 km. In the southern basins of the Baltic Sea; the dissolved oxygen (DO) content is permanently below 2 mg/l at depths below 80 m. DO contents vary seasonally with high values during winter and early spring times as opposed to lower values during summer and autumn periods. During late summers, the decline in DO content appears related to the extensive algae blooming consuming oxygen through the decomposition process. The LCSs map the patterns of Algae blooms detected by satellites. The duration of Algae blooming agrees with the persisting time of LCSs as well as the spatial surface water extents. The major 2003 inflow (MBI) increased the seabed DO content only in the lower part of the Arkona Basin that lasted just for about 3 weeks. The inputs of DO from the rivers and the 2003 MBI were not sufficient to counteract the seabed hypoxia in the Baltic Proper for the years 2000-2009.