Jeremy Bruno is a tech writer who blogs about ecology, evolution, conservation and culture at The Voltage Gate. Visit the 
From the University of Minnesota:
The reduction in species diversity occurs because increasing the amounts of limiting resources, such as nitrogen and water, makes an ecosystem more homogeneous and consequently reduces the number of opportunities for competing species to coexist. Put another way, it reduces the number of niches, allowing a few species to dominate.
[...] "In essence, the data in the article strongly supports a new explanation for why the world contains so many species," said Tilman. "It shows that plant diversity is directly related to the number of limiting factors (such as soil moisture, nitrogen, phosphorous, potassium and water)."It also helps explain why grasslands, lakes and rivers that are polluted with nitrogen and phosphorous (usually from agriculture) have fewer species. The reduction of species where the Mississippi River empties into the Gulf of Mexico is one of the best known examples of this phenomenon.
[...] "Our results show that the loss of plant species from a habitat due to nutrient pollution can persist for more than 100 years," Harpole said. "Thus human actions that simplify habitats can lead to long-term loss of biodiversity."
This is the main problem that we've been having with Chesapeake Bay as well. The Bay in inundated with nutrients and runoff from farms in central MD and PA, combined with the extensive waste from chicken farming on the Eastern Shore. This has disrupted the niche system of the Bay and even created extensive dead zones, incapable of supporting life.
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