[chopperman]

I would think that a sea-level canal would have some horrendous currents.

[jdege]

It has always had some ecologists worried about invasive species.

[Ozark Tom]

Speculation holds that ocean circulation changes resulting from the closing of a straight occupied by current day Panama started the current ice age.

http://geology.utah.gov/surveynotes/gladasked/gladice_ages.htm

Some believe reverting to the previous circulation pattern would be beneficial in the long view.

http://dissention.wordpress.com/2012/03/12/advantages-of-destroying-the-isthmus-of-panama/

Much closer to home and at a smaller scale, a similar event nearly came to pass in 1973.

http://www.forbes.com/sites/christopherhelman/2011/05/16/is-this-the-year-the-atchafalaya-river-captures-the-mississippi/

Tidal currents?