Abstract: We present a model-reduced variational Eulerian integrator for incompressible fluids, which combines the efficiency gains of dimension reduction, the qualitative robustness of coarse spatial and temporal resolutions of geometric integrators, and the simplicity of sub-grid accurate boundary conditions on regular grids to deal with arbitrarily-shaped domains. At the core of our contributions is a functional map approach to fluid simulation for which scalar- and vector-valued eigenfunctions of the Laplacian operator can be easily used as reduced bases. Using a variational integrator in time to preserve liveliness and a simple, yet accurate embedding of the fluid domain onto a Cartesian grid, our model-reduced fluid simulator can achieve realistic animations in significantly less computational time than full-scale non-dissipative methods but without the numerical viscosity from which current reduced methods suffer. We also demonstrate the versatility of our approach by showing how it easily extends to magnetohydrodynamics and turbulence modeling in 2D, 3D and curved domains.