Water monitoring is important in many fields, such as understanding the mechanism of water circulation of the earth ecological system, estimation of water pollutant, and effect of bridge construction on river. To monitor water resource with high accuracy and to reduce monitoring time and costs, this paper shows a new concept of mobile monitoring sensors, control method of the sensors, and estimation method for flow field. The proposed mobile monitoring sensor has actuators and screws. Thus it can move by itself. As a consequence, the cost for initial arrangement of sensors which is done by human becomes almost zero. For long time monitoring, it is necessary to prolong battery life. For this purpose, we propose a control method for distribution of sensors with low energy consumption. The proposed control can reduce input energy by using the drag force from flow field effectively for sensor's movement. In addition, for effective monitoring, we will propose on-line estimation method for the flow field. Finally, numerical examples show that the proposed monitoring is very effective in terms of both the energy consumption and estimation accuracy. This paper is the first attempt to propose the effective monitoring which includes a new concept of sensor, control method for sensor's movement, and estimation method for the flow field.