The invention discloses a water taking system for a shallow water river in a water-depleted mountainous area. The system involves an overflow weir, a water taking chamber and a radiation well, whereina spillway grid is arranged at an inlet of the water taking chamber, a floating mushroom head automatic water taking device and an on-line turbidity meter are arranged in the water taking chamber, and a submersible pump is arranged in the radiation well. When flooding does not occur, the overflow weir lifts the water level of the shallow water river, river water flows into the water taking chamber through the spillway grid, and then enters a water conveying pipe from the floating mushroom head automatic water taking device to flow to the radiation well, and finally, the submersible pump conveys the river water to a subsequent water purifying structure; a drought period relies on joint recharge of the above mentioned surface water recharge mode and the seepage of the radiation well; when the on-line turbidity meter in the water taking chamber during a flood period is displayed higher than 5 NTU, the on-line turbidity meter feeds back a signal to a self-control system, an electric butterfly valve mounted on the water conveying pipe is closed, and the radiation well supplies water through the self-seepage; according to the water taking system, the water supply amount of the shallow water river in the water-depleted mountainous area can be ensured, the water quality is reliable, the service life of the water taking system is prolonged, and the water taking cost is reduced.