A substrate processing apparatus includes a processing tub, a storage, a liquid recovery unit, a storage drain line and a liquid recovery unit drain line. The processing tub is allowed to accommodate therein multiple substrates, and configured to store therein a processing liquid. The storage is connected to the processing tub, and configured to store therein the processing liquid drained from the processing tub. The liquid recovery unit is configured to receive the processing liquid overflown from the processing tub. The storage drain line is configured to drain a liquid stored in the storage. The liquid recovery unit drain line is configured to drain a liquid received from the liquid recovery unit to an external drain line provided at an outside.