Hi Kape,
German texts have a tendency to abbreviate EU Directives as very short acronyms which we are less likely to do in English. Whereas RL is a common abbreviation of Richtlinie, English struggles to have a similar abbreviation.
In your case, if from the context it is clear that an EU Directive is at issue, then I would go with Colin's suggestion and simply write "Floods Directive" (as the Commission does on its website) and call the other one the "Water Framework Directive (WFD)" as does the Commission.
http://ec.europa.eu/environment/water/index_en.htmPaul