Physics-based fluid control has long been a challenging problem in balancing efficiency and accuracy. We introduce a novel physics-based fluid control pipeline using Laplacian Eigenfluids. Utilizing the adjoint method with our provided analytical gradient expressions, the derivative computation of the control problem is efficient and easy to formulate. We demonstrate that our method is fast enough to support real-time fluid simulation, editing, control, and optimal animation generation. Our pipeline naturally supports multi-resolution and frequency control of fluid simulations. The effectiveness and efficiency of our fluid control pipeline are validated through a variety of 2D examples and comparisons.