Who regulates farmland in Washington State - Army Corps of Engineers

You are most likely to meet the Army Corps if your land lies within the 100 year floodplain of any river, or is downstream from a dam that they maintain. 

Their regulatory powers come from the rivers and harbors act of 1899 and from the Clean Water act of 1976, and my involvement with that has centered around the dikes surrounding the island where my farm is located. 

The Army corps, of all of the regulatory agencies, the most farm-friendly in my opinion.  This isn't because they're less rigorous -- they can put you through the ringer, too, but the laws that they are charged with enforcing recognize and have exemptions for most common farming activities.  Stuff like tilling and plowing and mulching and so on.  They don't want you to "create upland conditions" -- raise your land above the flood plain by filling, for instance -- but most of your farm activities won't run afoul of their laws.