In this work, we propose a second-order accurate scheme for shallow water equations in general covariant coordinates over manifolds. In particular, the covariant parametrization in general covariant coordinates is induced by the metric tensor associated to the manifold. The model is then re-written in a hyperbolic form with a tuple of conserved variables composed both of the evolving physical quantities and the metric coefficients. This formulation allows the numerical scheme to i) automatically compute the curvature of the manifold as long as the physical variables are evolved and ii) numerically study complex physical domains over simple computational domains.