The ecosystem and country search facility of Fishbase (www.fishbase.org) provides a fantastic starting point for identifying combinations of fish for biotope aquariums that I think many experienced aquarists are familiar with.
Identifying aquatic plants that are native to the same areas is much harder and seems to rely on hearsay on online aquarium forums as much as anything else. I just came across a great resource from the Senckenberg Museum in Frankfurt that lists aquatic plants in different parts of Africa as part of a wider guide to African plants. To filter for aquatic plants, you need to hit ‘Browse and Search’, scroll down to ‘Life Form’ under the heading ‘Habit’ and select ‘Hydrophyte’ (or ‘Halophyte’ if you are looking for brackish water or coastal species). Also helpful to untick the ‘Only search for species with pictures’ to get a fuller list. Not sure how complete the database is but provides a great starting point.
You can access the guide at http://www.westafricanplants.senckenberg.de/. You can also search for East Africa, Central Africa and Africa as a whole through the links on the homepage.