It is possible to reduce flood risk in estuaries without having to drastically modify the river banks by levees or to block shipping routes and ecological flows by dams. ‘Storm surge barriers’ close off a river mouth at times of high sea water levels, but keep the river open during calmer times. ‘Moveable river flood barriers’ direct a river towards less urbanised parts of the delta. It is likely that with climate change and continuing economic growth more of these barriers will be built worldwide. The influential Dutch state commission the ‘Delta Commission’ has adopted an idea by Delft University of Technology to flood-proof the Dutch Rhine-Meuse delta by a number of existing and new moveable barriers. These will direct high water flows in desired directions, particularly at times when a storm at sea coincides with high river discharges. This would create a historically complex system of flood defenses, thus needing thorough modelling and more detailed design to evaluate benefits and costs. This paper will compare a number of alternatives as follows: locate the various barriers on different locations, see where additional river widenings would be possible, calculate the remaining required levee modifications (dictated by Dutch national flood law) as a function of sea level rise, determine the effects on urbanisation of the river banks, on shipping, and if possible also on ecological flows. This comparison will in this paper not lead to the ‘best configuration’, but to valuable insight in the system. It appears that improving the high water prediction errors and the location, failure probability, operating regimes and architecture of the barriers will increase benefits and reduce costs of the entire flood protection system. This paper follows from a multidisciplinary, explorative and practically-oriented research project (11 different researchers and consultants) conducted under the Dutch ‘Hotspot Rotterdam - Knowledge for Climate’ programme in 2010.