Stifel Nicolaus had anticipated profit of 10 cents a share; now, the analysts expect the company to only break even.
American Commercial Lines, which is headquartered in the Ohio River town of Jeffersonville, builds barges and ships ethanol and other products.
In the first quarter, the company turned a $2.3 million profit on revenue of $270.5 million.
Flooding has forced the closure of many locks on the upper Mississippi - affecting 10 percent to 15 percent of the company's fleet of dry-cargo barges, Stifel Nicolaus said.
The firm maintained its "buy" rating but decreased the target price of its stock by $1, to $18 per share.
Shares fell 3.9 percent this morning to $11.95.