The bottom line is that researchers aren’t exactly sure what causes “brown marsh” or coastal marsh dieback, as it is formally known. They speculate that it “may be cyclical depending on interactive climate conditions, sea level anomalies, and other biotic factors.” (http://www.nwrc.usgs.gov/about/capabilities/brwnmrsh.htm)

From what I’ve read, it appears to be related to drought conditions which cause increased salinities, which thus put increased stress on the marsh plants making them more vulnerable to disease and other factors.

Here are links to two websites that address the problem:
http://brownmarsh.com/default.htm
http://www.nwrc.usgs.gov/about/capabilities/brwnmrsh.htm

Also, here are links to fact sheets concerning brown marsh:
Brown Marsh Fact Sheets [http://brownmarsh.com/factSheets/index.htm]
Brown Marsh Fact Sheet: Facts about the salt marsh dieback in Louisiana: CWPPRA Task Force Fact Sheet, 1 p [http://brownmarsh.com/factSheets/brown%20marsh%20Fact%20sheet.pdf]