We develop the structure theory of symplectic Lie groups based on the study of their isotropic normal subgroups. The article consists of three main parts. In the first part we show that every symplectic Lie group admits a sequence of subsequent symplectic reductions to a unique irreducible symplectic Lie group. The second part concerns the symplectic geometry of cotangent symplectic Lie groups and the theory of Lagrangian extensions of flat Lie groups. In the third part of the article we analyze the existence problem for Lagrangian normal subgroups in nilpotent symplectic Lie groups.