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The primary ecological concern of dams is that they destroy habitats necessary for species survival. In China particularly, the construction of the Three Gorges Dam has caused the Chinese river dolphin and the Siberian crane to become critically endangered. additionally, the dam cuts the flow of nutrient supply, which lowers the ecological capacity of river ecosystems.
However, nutrient supply is not universally low; due to farming along the shoreline, which has caused NO3 and Potassium levels to double to unsafe levels toward the basin of the Yangtze River. Additionally, the prevalence of pesticides and herbicides, along from excretions from coal mines, has reached unsafe levels.
Unfortunately, the health of the Yangtze River is not looking so good. That is why it is important at this point to weigh the options. Without dams, pesticides and lead continue to pollute the river, while farming operations release unsafe levels of nutrients. Or the Chinese could continue to use dams, which reduce the reliance on coal mining and push economic focus away from agriculture, albeit forcefully.
While the health of a few exotic species my connect with the general public, it is important to try to minimize the overall ecological impacts, not just the ones that save a few famous ones.

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It's true. Dams are not pretty. But compared to the global stigma China faces today over their air quality, it a necessary sacrifice. With a growing and increasingly urban middle class looking to reap the promised benefits of the Cultural Revolution, it is vital for the government to clean up the skyline.
As stated in the Economic passage, it is undoubted that the construction of dams destroys homes along the shoreline and forces people to urban areas. Fortunately, it is predicted that sediment and flooding patterns should normalize by 2060. While this may seem like a long time, at least there is a timetable for ecological recovery, as opposed to coal mining, which causes irreparable damage to mining sites and the communities that surround them.
An issue that is hard to argue is food availability. The erratic flooding, while potentially nor permanent, will curtail the extent of Chinese agriculture for many years. However, we again need to look at the alternative: coal mining, which has been known to excrete runoff that poisons local crops. Again, we have to weigh what is better, a food shortage or a food poisoning.

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http://onlinelibrary.wiley.com/doi/10.1029/2005WR003970/full
http://www.journals.uchicago.edu/doi/abs/10.2307/3182195?journalCode=tcj
http://ageconsearch.umn.edu/bitstream/171896/2/HUANG.pdf
http://onlinelibrary.wiley.com/doi/10.1029/2006GL025800/full
http://www.sciencedirect.com/science/article/pii/S0048969708004713

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The primary claim against dams, and the Three Gorges Dam in particular, is that they are not cost effective. With a price tag of $10.4 billion dollars, it may seem like an impossible return on investment. However, the reality of the situation is that energy consumption is a real concern for the Chinese government that could not be resolved with the continuation of coal as their primary energy source. With energy consumption rates rising 56.6% between 2005 and 2011, the Chinese had to choose between an hefty price tag or a national disaster.
Additionally, the increase in energy supply counteracts the claim that the dam destroys jobs. While it does remove business from the shoreline, it also encourages people to move to the cities and take up more urban jobs. This has been a long term goal for China, who sees urban development as the key to progress and increased global competition. So while it may not be a deliberate attempt to remove jobs, dam production in China definitely represents their forward thinking economic policy.

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Dams are often labeled as an energy alternative no better than fossil fuels in terms of ecological preservation. The Three Gorges Dam is a common case study of this claim; built by the Chinese, the dam has caused irreparable environmental damage to the Yangtze River. Yet, compared to the disastrous effects of coal mining that has plagued the ecology of China in prior decades, dams remain a necessary evil in developing countries.