We describe a strongly coupled layered system in 3+1 dimensions by means of a top-down D-brane construction. Adjoint matter is encoded in a large-Nc stack of D3-branes, while fundamental matter is confined to (2 + 1)-dimensional defects introduced by a large-Nf stack of smeared D5-branes. To the anisotropic Lifshitz-like background geometry, we add a single flavor D7-brane treated in the probe limit. Such bulk setup corresponds to a partially quenched approximation for the dual field theory. The holographic model sheds light on the anisotropic physics induced by the layered structure, allowing one to disentangle flavor physics along and orthogonal to the layers as well as identifying distinct scaling laws for various dynamical quantities. We study the thermodynamics and the fluctuation spectrum with varying valence quark mass or baryon chemical potential. We also focus on the density wave propagation in both the hydrodynamic and collisionless regimes where analytic methods complement the numerics, while the latter provides the only resource to address the intermediate transition regime.