One of the areas of engineering protection of lands from flash floods is the use of intercepting waterworks on the side tributaries, which help to reduce the peak of the flood on the main river and redistribute it over time. With an increase in rainfall, flood protection capacity of existing or designed structures may not be enough to transform the river flow. The paper considers a mathematical model of flow control by a system of reservoirs, where a part of the accumulating capacity of the flood protection structure on the side tributary is redistributed into gabion waterworks located upstream of the river. This model allows to clarify the parameters and modes of operation of waterworks and evaluate their functioning, considering current and future economic and environmental conditions.