The legislation introducing the septic tank charge has been passed in the Dáil by 76 votes to 34.
The Water Services (Amendment) Bill, which will require owners of septic tanks to pay a fee in order to register it for inspection, will now go back to the Seanad for final approval next week.
There was heated discussion within the Dáil chamber as the issue was debated, with Sinn Féin's Mary-Lou McDonald calling for more information on what septic tank inspections would entail.
Fianna Fáil's Éamon Ó Cúiv said the charge was unfair as only those in rural areas would be liable.
However Tanaiste Eamon Gilmore said people had no reason to worry over the new charge and accused opposition TDs of whipping up people's fear around the matter.
Minister for the Environment Phil Hogan also denied suggestions that the charge could be increased once brought into law and pointed out that the €50 fee was written into the legislation.
He added that the inspections will be carried out by local authority engineers and if they need to employ assessors from outside, they can do so.
The minister said he will look very carefully at the EPA guidelines laid down for the inspections and they will be implemented by the local authorities.
Earlier Independent TD Luke Ming Flanagan had said he does not agree with a fee being charged on householders.
Mr Flanagan said they would be paying more money to local authorities, who are not accountable and who will squander it.
Speaking in the Dáil, during the final hour of debate on the Water Services Amendment Bill, he said that the new legislation is not about clean water, but about making money.