In this paper, the problem of automatic control of pollutant on a shallow river using surface water systems is addressed using a benchmark test case based in the Ebro River. The Ebro River presents flooding episodes in the city of Zaragoza in Spring when snow melts in the Pyrenees. To avoid flooding and high pollutant levels in living areas, some lands outside the city are prepared to be flooded. Going one step further, this paper is focused on the pollutant level control at a certain point downstream of the river under flooding episodes, and several control strategies for that purpose are presented and tested.