HONOLULU -- Federal and state agencies have reached an agreement with the Hawaii Department of Transportation over storm water violations that will end up costing the state about $52 million.

When it rains, runoff from state highways and state transportation yards and construction sites goes into streams and gullies and eventually into the ocean. If it's full of contaminants like oils or chemicals, there's damage to the environment.

The EPA snapped photos of environmental violations at state construction yards, contaminated runoff at a state auto shop on Kauai and weeds growing out of a storm drain, which could lead to it getting clogged.

The violations stretch back to 1999, three years before Gov. Linda Lingle took office.

"We don't want to blame the previous administration; it was done a few years ago. We've taken a proactive stance to make sure it doesn't happen under this administration," state Department of Transportation Director Rod Haraga said.

The DOT is splitting a $1 million fine between the EPA and the state Health Department.

"Storm water discharges can contain contaminants like oily wastes, chemicals and sediments. And sediments in particular are very harmful to areas like coral reefs," EPA spokesman Dean Higuchi said.

The state also agreed to spend $50 million over five years to cut down on storm water runoff.

The state is also training its staff and tenants about controlling polluted runoff.

"Over the period of time, they've improved on their plans and procedures, but we really wanted them to make sure that they were altogether and solid from preventing any contaminants from getting into storm water discharges, getting into the ocean," Higuchi said.

The state DOT said it is already inspecting highway construction projects more frequently than before to ensure chemical runoff doesn't enter storm drains. The state has added a $3 million drain-cleaning contract in addition to regular drainage maintenance.