A hydraulic control system for a machine is disclosed. The hydraulic control system may have a tank, a pump configured to draw fluid from the tank and pressurize the fluid, a swing motor configured to receive the pressurized fluid and swing a body of the machine relative to an undercarriage, and a tool actuator configured to receive the pressurized fluid and move a tool relative to the body. The hydraulic control system may also have an energy recovery device configured to convert hydraulic energy to mechanical energy, a first accumulator configured to store waste fluid received from the swing motor, and a second accumulator configured to store waste fluid received from the tool actuator. Stored waste fluid from at least one of the first and second accumulators may be selectively discharged into the energy recovery device.