Yeah the earth is a very complex system. When YC came out and proposed the idea of proposed turning the Sahara into a bunch of algae ponds [1] I cringed. First the plan requires more power than we currently produce just to pump all the water but then you would drastically reduce how much gets blown over to the Amazon AND you would suddenly introduce a tremendous amount of moisture to the atmosphere which would almost certainly change global weather patterns.
All of that moisture could cause a considerable increase in rainfall for somewhere (presumably the Amazon, I don't know anything about weather modelling though and am just guessing) which could be catastrophic for life there and even result in tremendous economic losses.
Even relatively small scale geoengineering like damns can have profound negative impacts on ecosystems with some being very predictable and some being completely wildcard. We know the Sahara fertilizes the Amazon but what level does it effect marine life by feeding stuff at the bottom of the food chain (plankton for example) and what would removing that mineral/nutrient source do to the food chain, would it increase rains (and cloud cover) over that area of ocean that might change temperatures subtly enough to make an impact on currents, etc. We're at the point now as a species where we have the power of gods but can't begin to understand the implications of what we are capable of doing.
[1] http://carbon.ycombinator.com/desert-flooding/