Dear Victor,

One way could be shading that area of water sheet, where there is heavy concentration of algae, as a little over 3 days of total light shading can kill the plants. Another way could be to minimise nutrient flow from catchment area wherefrom waters empties into the water body. A third way would be to introduce filter feeders into the system, which would take care of phytoplankters from the system.Algae consuming fish varieties can also be cultured in batteries of floating cages in these water bodies which would bring down algal biomass. The design of the embankments could be made in such a way that the wafting of wind would naturally push the algal mass to a certain collection point, from where they can be taken out periodically. 

If the lake in question is shallow with a long fetch, then raising the water level could help decrease internal nutrient loading. See Nagid, E.J., D.E. Canfield, Jr. and M.V. Hoyer. 2001. Wind-induced increases in trophic state characteristics of a large (27 km2), shallow (1.5 m mean depth) Florida lake. Hydrobiologia 455:97‒110.

Algaestats will be a good option. It does not kill algae but it inhibits their growth.

I use this as a start point reference in classes for basin controls. http://www.tandfonline.com/doi/abs/10.1080/07438140109354128

The options that you can go through are really dependent on your reservoir characteristics, location, final use etc.

Bacillus bacteria are used to control algae specially cyanobacteria. You need to focus on nutrients loading from the surrounding specially NO3-N for control of algal growth. Pl have a look on the following attached article. Regards

Dear Victor,

Presently I am also trying to figure out this problem. My team is working on bioremediation of a hypereutrophic lake. We are dosing bacterial consortium in the lake to improve biodegradation of organics and to reduce nutrients. But results are  good but very slow. Can you suggest anything better.