The fine equated to only about $1.35 per day for each day Francis M. Palma’s house posed a health threat in Ocean Heights. Even so, over 12 years that adds up to a hefty sum.

And the $6,000 he was ordered to pay by the Edgartown board of health last Thursday is only a small part of the total cost of Mr. Palma’s long defiance of town authorities.

Add in possibly $20,000 for a new wastewater disposal system, plus the cost of bringing town water to his property and making connection available to his neighbors, the expense of remodeling the house and legal fees.

Edgartown health agent Matt Poole said it was an unprecedented penalty, the first time a substantial fine had been levied on a homeowner who has twice breached undertakings relating to the size of a house and the treatment and disposal of wastewater from it.

And it came at the end of an unprecedented case, which had begun way back in August 1995.

That was when Mr. Palmer and Susan Shea bought the old one-bedroom house on the Boulevard and got a permit to do some renovation work.

“The next anyone knew, the old house was gone and he was preparing to construct a much larger new house,” Mr. Poole said.

The Edgartown conservation commission issued a cease and desist order, but work was later allowed to proceed after the owners agreed to the stipulations of the board of health that the house, according to the plans provided to the town, would have only one bedroom.

The health board also gained assurances that the failed septic system would be regularly maintained, a new well dug, and the house would tie into a shared wastewater disposal system.

But the house was eventually expanded to include three bedrooms and two full bathrooms — discovered only during a 2005 inspection by Mr. Poole — and the septic issue was never satisfactorily addressed.

After repeated breaches in the past, the town got serious this time.

“The decision will be in the form of a recordable document at the registry of deeds. That will be a very public document,” Mr. Poole said.

And to ensure that the interior modifications reducing the size of the house from the current three back to two bedrooms are properly carried out — and stay carried out — Mr. Poole said a deed rider, or covenant, will go on rec-ord at the registry that will allow the board of health to enter with reasonable notice to inspect the house.

The precise wording of the document is yet to be worked out between town counsel and the attorneys acting for the homeowners, but Mr. Poole said he was very happy with the outcome.

“We imposed a penalty of $6,000. Town water will have to go in post haste, [although] this is somewhat subject to the water department schedule. The house is to be modified to present itself as no more than a two-bedroom house, which means taking down a wall to remove a bedroom. And next June 1 is the deadline for construction of the septic system,” Mr. Poole said.

The enhanced treatment system will reduce nitrates leaching into the groundwater and potentially into Sengekontacket Pond. Both the inflow of effluent into the new system and the outflow will be monitored regularly to safeguard the pond’s health.

Mr. Poole said the case showed the seriousness authorities now attach to issues of contamination of the pond.