Quantum sensing and computation can be realized with superconducting microwave circuits. Qubits are engineered quantum systems of capacitors and inductors with non-linear Josephson junctions. They operate in the single-excitation quantum regime, photons of $27 \mu$eV at 6.5 GHz. Quantum coherence is fundamentally limited by materials defects, in particular atomic-scale parasitic two-level systems (TLS) in amorphous dielectrics at circuit interfaces.[1] The electric fields driving oscillating charges in quantum circuits resonantly couple to TLS, producing phase noise and dissipation. We use coplanar niobium-on-silicon superconducting resonators to probe decoherence in quantum circuits. By selectively modifying interface dielectrics, we show that most TLS losses come from the silicon surface oxide, and most non-TLS losses are distributed throughout the niobium surface oxide. Through post-fabrication interface modification we reduced TLS losses by 85% and non-TLS losses by 72%, obtaining record single-photon resonator quality factors above 5 million and approaching a regime where non-TLS losses are dominant. [1]M\"uller, C., Cole, J. H. & Lisenfeld, J. Towards understanding two-level-systems in amorphous solids: insights from quantum circuits. Rep. Prog. Phys. 82, 124501 (2019)