This paper proposes an IoT active acoustic system for fish monitoring with direct application in biodiversity preservation near hydropower plants and dams. The system employs a cost effective single board computer as central processing unit. The acoustic signal processing is performed at two levels: the first at the board level (embedded), to decide upon transmission of data to a server, and the server level to show the results of detection and the number of fish passages (acoustic signature analysis). The performance analysis of the proposed fish monitoring system is carried out during a four days experimental campaign in Chatou, France.