The bank will provide a US$8.5mn loan and a US$205,000 grant.
Nearly US$40bn in investments is frozen due to unfinished works.
The frontrunner has declared his intention to go ahead with unfinished projects.
Alberto Carrasquilla, who also served as finance minister during the Álvaro Uribe administration, is accused of profiting from a water bonds program.
The public works ministry will modify the framework for the initiatives, which will include partial funding of studies by the state and higher premiums for those who propose them.
The project is crucial to guarantee water supply in Brazil's drought-stricken northeast region.