In this paper we consider a new geometric approach to Madelungs quantum hydrodynamics (QHD) based on the theory of gauge connections. Unlike previous approaches, our treatment comprises a constant curvature thereby endowing QHD with intrinsic non-zero holonomy. In the hydrodynamic context, this leads to a fluid velocity which no longer is constrained to be irrotational and allows instead for vortex filaments solutions. After exploiting the Rasetti-Regge method to couple the Schrodinger equation to vortex filament dynamics, the latter is then considered as a source of geometric phase in the context of Born-Oppenheimer molecular dynamics. Similarly, we consider the Pauli equation for the motion of spin particles in electromagnetic fields and we exploit its underlying hydrodynamic picture to include vortex dynamics.