The head of the project called Kopacki-rit.com, Akos Papp, and the head of the project Fauna.hr, Gorjan Agacevic, received the awards in the categories e-education and e-science respectively.
Kopacki Rit is a nature park in eastern Croatia.
At the three-day summit which is taking place in the capital Tunis, Croatia is also presenting the government's one-stop shop project called Hitro.hr.
Croatian President Stjepan Mesic addressed the summit on Wednesday.
"One needs to reconcile freedom of the information and the need to introduce control over information, Mesic said.
"We must not lose sight of the fact that information society has the potential to become a nightmare instead of a blessing," he added.
The Tunis event is the second phase of a summit held in Geneva two years ago. It pooled 50 heads of state and prime ministers and more than 11,000 officials, information technology experts and business managers from wealthy and poor countries alike so as to set in motion a UN initiative aimed at increasing access to modern telecommunications and the Internet in developing countries.