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Abstract There is tremendous interest in employing collective excitations of the lattice, spin, charge, and orbitals to tune strongly correlated electronic phenomena. We report such an effect in a ruthenate, Ca₃Ru₂O₇, where two phonons with strong electron-phonon coupling modulate the electronic pseudogap as well as mediate charge and spin density wave fluctuations. Combining temperature-dependent Raman spectroscopy with density functional theory reveals two phonons,B₂^PandB₂^M, that are strongly coupled to electrons and whose scattering intensities respectively dominate in the pseudogap versus the metallic phases. TheB₂^Psqueezes the octahedra along the out of planec-axis, while theB₂^Melongates it, thus modulating the Ru 4d orbital splitting and the bandwidth of the in-plane electron hopping; Thus,B₂^Popens the pseudogap, whileB₂^Mcloses it. Moreover, theB₂phonons mediate incoherent charge and spin density wave fluctuations, as evidenced by changes in the background electronic Raman scattering that exhibit unique symmetry signatures. The polar order breaks inversion symmetry, enabling infrared activity of these phonons, paving the way for coherent light-driven control of electronic transport.