We derive a linearized rotating shallow water system modeling tides, which can be discretized by mixed finite elements. Unlike previous models, this model allows for multiple layers stratified by density. Like the single-layer case [R. C. Kirby and T. Kernell, Comput. Math. Appl., 82 (2021), pp. 212–227], a weighted-norm preconditioner gives a (nearly) parameter-robust method for solving the resulting linear system at each time step, but the all-to-all coupling between the layers in the model poses a significant challenge to efficiency. Neglecting the inter-layer coupling gives a preconditioner that degrades rapidly as the number of layers increases. By a careful analysis of the matrix that couples the layers, we derive a robust method that requires solving a reformulated system that only involves coupling between adjacent layers. Numerical results obtained using Firedrake [F. Rathgeber et al., ACM Trans. Math. Software, 43 (2016), 24] confirm the theory.