Beginning on July 1, the tax on flushing a toilet in Maryland will double, generating millions of dollars more to help restore the Chesapeake Bay.

The Chesapeake Bay Restoration Fee, known as the flush tax, will increase from $30 per year to $60. The Maryland General Assembly passed the increase.

The fee is used to upgrade the state’s 67 major sewer treatment plants that discharge into tidal waters, upgrade failing septic systems and fund cover crops for fields — all to improve the health of the Chesapeake Bay.

In St. Mary’s County, the flush tax is applied to the property tax bills of homeowners using septic systems. A $2.50 fee is added to the monthly bills for customers of the St. Mary’s Metropolitan Commission, which operates public water and sewer systems.

The flush tax will go to $5 per month on MetCom bills. MetCom customers are also scheduled to have increases in their monthly bills beyond the flush tax increase — about $4.50 more per month for residential customers, to cover the rising costs of maintaining the systems.

MetCom has 14,029 public water customers and 11,779 sewer customers.

Of the 37,064 households in St. Mary’s, 70 percent, or 26,071, are on septic systems, according to the county’s Department of Land Use and Growth Management.

The largest sewage treatment plant in St. Mary’s is the Marlay-Taylor Wastewater Reclamation Facility in Lexington Park. It has a capacity of 6 million gallons a day, but the average flow is 4 million gallons, said Dan Ichniowski, deputy director of MetCom.

All 67 of Maryland’s major sewage treatment plants have to upgrade from biological nutrient removal to the enhanced nutrient removal process to reduce the load of nitrogen and phosphorus discharged into the Chesapeake and its tributaries. Those nutrients harm water quality.

The design for the Marlay-Taylor upgrade is finished, said Jacquelyn Meiser, director of MetCom; bids for the work go out in June.

“All things are going smoothly,” Ichniowski said of the $36 million project.

Construction should be finished in 2014, well ahead of the state’s 2017 deadline.

The flush tax provides $10.6 million for the project. MetCom is borrowing the rest.

The $30 annual flush tax wasn’t collecting enough money to complete the work on the state’s major sewage treatment plants, Meiser said.

“There just wasn’t enough money in there . . . and these costs have gotten a lot higher,” she said.

Doubling the flush tax will produce at least $54.6 million more in fiscal 2013, according to a fiscal analysis by the Maryland Department of Legislative Services. The money will continue to increase as the state’s population grows.

The $30 flush tax generated $382.5 million so far for the state, and has supported upgrades to 23 sewage treatment plants. However, engineering estimates put the cost of all upgrades at $1.38 billion. The fee also generated $92.5 million to be used to upgrade failing septic systems and to buy cover crops.

Del. John Bohanan (D-St. Mary’s) was the only representative of St. Mary’s to vote in favor of the increase to $60 per year.

“When the original flush tax was adopted, we knew it would not be sufficient. This allows us to continue to complete it. This is all about making sure we clean up the bay. For an additional $3 we get to significantly progress on the health of the bay,” Bohanan said Friday.

The public hearing on increasing MetCom’s monthly rates was Monday.