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."
Developers hoping to build a £100m hydro power plant in a disused Gwynedd quarry have been granted environmental permits.