Birnbaum and her agency have endured scathing criticism in the weeks since the Gulf oil spill over alleged lax oversight of drilling and what President Barack Obama has called an overly cozy relationship with industry.
Salazar said that Birnbaum resigned on her own terms and of her own volition.
Her departure came just hours before a news conference where Obama plans to address the spill and announce new safety protocols and an extension of a deepwater drilling moratorium.