A common way to waterproof flat, or nearly flat roofs is to use single-ply membrane coverings, which either adhere straight to the roof deck, or are fixed with special mechanical fasteners. A major manufacturer of these is Sarnafil - lots more information can be found on their website http://www.sarnafil.co.uk. Membrane roofing is ideal for medium to large flat roofs, as well as being particularly useful for covering awkward geometry such as curves.
The simplest way of using a membrane roof is illustrated below, with an AutoCAD drawing of the same detail available to download at the end of this article.
Care must of course be taken at the edges of the roof, to create a fully waterproofed construction - see this article, which details a possible edge condition, or the construction details on the Sarnafil website.
Source: Professional architect's drawings