Is Hydroelectric Power actually a "Green" Energy Source?

Source: Tennessee Valley Authority (public domain)

Greenhouse gases are gases that trap heat in the atmosphere, and the three major greenhouse gases are carbon dioxide, methane, and nitrous oxide. Natural sources of these gases consists of lakes, rivers, streams, and ponds as well. Lakes are environmentally beneficial because they are active, changing, and are important regulators of the three major greenhouse gases. That being said, lakes and reservoirs are known to be built for the purpose of generating power. So much so that water has been retained by dams that the global sea level rise has lowered approximately 0.02 inches per year in the span of 50 years. And since fossil fuels are not utilized to to produce hydroelectric power, lakes are known for their "green" energy sources alternative. Which is a common misconception because it is those lake and reservoirs that release powerful greenhouse gases into the atmosphere as well. Could hydroelectric dams still be considered a "green" energy source even though they are releasing enormous amounts of heat trapping gases? 

When reservoirs are being constructed for power generation, soils, plants, and trees are flooded. This cause of decay in plants and soil material can potentially contribute to colossal distribution of carbon dioxide and methane during the first few years of forming the establishment. Various studies have analyzed and shown that 3-10 times more greenhouse gases are produced by recently built reservoirs than from natural lakes of about the same size in the first 2-5 years after a reservoir is built. Of course, they release more greenhouse gases from its initial point of construction as lakes and reservoirs recommence the release of carbon dioxide and methane to generate power. As carbon dioxide and methane enhanced water flow through turbines, hydrostatic pressure drops as a vast portion of gas expeditiously escapes to the atmosphere. Some places like tropical reservoirs can even release more greenhouses gases than fossil fuel alternatives. 

Although lakes and reservoirs utilized to produce hydroelectric power release greenhouse gases, they generally let out considerably less amount of fossil fuel based power plants. And even though hydroelectric is not the perfect "green" energy source, it is still a much more substantially friendly alternative and can play a role in alternative energy solutions plan.  

References: 

Williamson, C. E., Saros, J. E., Vincent, W. F., & Smol, J. P., et al. 2009. Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnology and Oceanography, 54, 2273-2282.