In the assessment of complex spatial planning projects, the ecological impacts and socio-economic impacts are fundamental to the evaluation. The measurements of ecological impacts of spatial plans have to be integrated in a standardised way. In the present paper, we analyse two Dutch case studies and apply the standardised Threat-Weighted Ecological Quality Area measurement. This measurement is developed to evaluate projects with terrestrial impacts but has not yet been applied for water evaluations. We aim to show how the use of a common measurement tool incorporates both ecological quality and degree of threat on criteria in the EU Water Framework Directive and Nature 2000. The measurements discussed here derive from two cases of cost-benefit analysis: The first case is the Markermeer, the second largest lake of The Netherlands, and a study on water quality improvement and nature restoration; an artificial island will also be the setting for a new residential area. The second case study is on water level management carried out on the IJsselmeer, the largest lake in the country. Results of our analysis show the potential impacts with a standardised method to the spatial distribution and quality of the ecosystems.