The statistical mechanics of arbitrary holonomic scleronomous systems subjected to arbitrary external forces is described by specializing the Lagrange and Hamilton equations of motion to those of the Brownian motion on a manifold. In this context, the Klein-Kramers and Smoluchowski equations are derived in covariant form, and it is demonstrated that these equations have equilibrium solutions corresponding to the Gibbs distribution, in agreement with standard thermodynamics. At last, the Langevin dynamics corresponding to the Smoluchowski limit is found to exactly correspond to the Brownian motion on a smooth manifold. These results find significant applications in the study of several statistical properties of constrained molecular assemblies (e.g. polymers) of interest in chemistry, physics and biology.