We present a Lagrangian-Eulerian scheme to solve the shallow water equations in the case of spatially variable bottom geometry. This work was dictated by the fact that geometrically Intrinsic Shallow Water Equations (ISWE) are characterized by non-autonomous fluxes. Handling of non-autonomous fluxes is an open question for schemes based on Riemann solvers (exact or approximate). Using a local curvilinear reference system anchored on the bottom surface, we develop an effective first-order and high-resolution space-time discretization of the no-flow surfaces and solve a Lagrangian initial value problem that describes the evolution of the balance laws governing the geometrically intrinsic shallow water equations. The evolved solution set is then projected back to the original surface grid to complete the proposed Lagrangian-Eulerian formulation. The resulting scheme maintains monotonicity and captures shocks without providing excessive numerical dissipation also in the presence of non-autonomous fluxes such as those arising from the geometrically intrinsic shallow water equation on variable topographies. We provide a representative set of numerical examples to illustrate the accuracy and robustness of the proposed Lagrangian-Eulerian formulation for two-dimensional surfaces with general curvatures and discontinuous initial conditions.