Snowdonia Pumped Hydro (SPH) is awaiting a planning decision for the scheme at Glyn Rhonwy in Llanberis.
Natural Resources Wales (NRW) has given permission to empty standing rainwater from two disused quarries at the site into Nant y Betws and Llyn Padarn.
It said the permits have been issued with "strict conditions".
Plans for the 99.9MWe hydro plant are being considered by the UK Planning Inspectorate, with a decision expected by early March.
NRW said it was satisfied that the company will "operate safely without harming the environment or local communities."
SPH said the drainage of rainwater was necessary before work can begin to sculpt the quarries that will form the upper and lower reservoirs.
Their application to fill the reservoirs once they are completed by gradually abstracting water from Llyn Padarn lake has already been approved.
Opponents of the scheme claim standing water in the lower quarry where ordnance was dismantled by the RAF in the 1970s may be contaminated.
But SPH said independent sampling and testing of both surface and ground water at the site "show no evidence of contamination."

About 40,000 homes have been damaged by floods caused by heavy rains, and 20,000 people have been rescued.
In Livingston Parish, home to 138,000 people, officials estimate that 75% of homes have been completely destroyed.
Residents returning to their homes are finding standing water, mould, and pest infestations, while the threat of further flooding and rainfall remains.
David Key arrived at his house in Prairieville by boat this morning to find five inches (12.7 cm) of "muddy nasty bayou water".
"I'm not going to lie, I cried uncontrollably," he said. "But you have to push forward and make it through. Like everybody says, you still have your family."
The National Weather Service is predicting that the chance of thunderstorms will continue in the region throughout the week, with temperatures expected to reach 32C (92F).
At an afternoon press conference in Baton Rouge, Louisiana Governor John Bel Edwards updated the death toll to eight people, and described how emergency crews are continuing with rescues.
"Nobody is going to be forgotten and we're going work around the clock," Mr Edwards said, calling the disaster a "historic flooding event".
"It's unprecedented," he told reporters. "We understand that there are a lot of people who are suffering."
Emergency crews are checking washed away cars for the bodies of motorists who may have become trapped inside.
Floodwaters have been receding today in most of the effected areas, however water levels are rising in the southern parts of the state as the excess water washes downriver and out to sea.

The CPS is considering files sent by police following investigations in up to 27 constituencies.
It relates to claims some campaigning costs in the 2015 general election were wrongly recorded.
The Conservative Party has insisted administrative errors were to blame rather than any intention to deceive.
And it has said some of the spending was correctly declared.
It is alleged the Conservatives spent tens of thousands of pounds on local campaigns - including on "battle bus" visits by activists - which were either not declared or were wrongly registered as national spending.
The allegations came to light following an investigation by Channel 4 News.
Under complex election spending rules, parties must disclose national spending separately from money used to promote each candidate, and separate national and local limits apply.
Up to 16 police forces across England have submitted files to be considered by prosecutors.
The CPS will consider whether there is sufficient evidence of a breach in the law, and whether a prosecution is "in the public interest".
If general election candidates are prosecuted the Conservative Party will have to decide whether to suspend them and replace them as nominees.
The last date for candidates to register for the election is 11 May.
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Developers hoping to build a £100m hydro power plant in a disused Gwynedd quarry have been granted environmental permits.
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Residents are beginning to return to their flooded homes, even as more rains are expected in the state of Louisiana.
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Prosecutors are expected to announce on Wednesday whether Conservative politicians or officials will face charges for breaches of expenses rules.