In Israel, which is a bottleneck for some six hundred million migrating birds, the drainage of the Hula Lake in the north resulted in serious conflicts between fish-eating birds and the intensive fish farming and agriculture that became established on the reclaimed land. Implementation of various deterrence methods, including lethal control, failed to solve these conflicts. We followed the concept that only by understanding the biology of the organism in question could the tools (indications) for effective and sustainable management be devised that would solve such conflicts while helping the preservation of natural assets such as wetlands and their inhabitants. We demonstrated this concept in the solutions reached in the case studies of pelicans and cormorants and their interactions with intensive commercial fish ponds. We studied the physiological condition, food preference and energy demands, and ecological constraints of Great White Pelican Pelecanus onocrotalus, Great Cormorant Phalacrocorax carbo and Pygmy Cormorant Microcarbo pygmeus. As a result, we suggested different management solutions that are currently implemented with the full cooperation of the fishermen and the nature preservation authorities. Based on assessment of visual acuity to detect and catch fish under water Great Cormorants were effectively pushed towards Lake Kinneret where they could hunt more profitable fish than in the turbid fish ponds. The established roosts there were not controlled such as to lead the birds away from the fishponds. In case of the pelicans, part of the drained Hula valley was reflooded and extra fish was provided. Both measures effectively reduced the damage at the fish farms. We have shown that such solutions are economically helpful for fishermen and enable the preservation of the wetland habitat.