"I have presented my resignation to the president, which he accepted," Salles, 46, told a news conference at the presidential palace in Brasilia.
Salles, one of the most divisive figures in far-right President Jair Bolsonaro's government, has presided over a surge in deforestation in the Amazon rainforest and major cuts to environmental protection programs since taking office in January 2019.
The minister had faced even greater scrutiny since May 19, when a Supreme Court justice ordered an investigation into allegations that he and top officials in his ministry helped companies traffic illegally logged rainforest wood to Europe and the United States.
Police raided his home and environment ministry offices the same day.
The ruling also granted investigators access to Salles's bank accounts and suspended 10 officials from their posts, including the head of the environmental protection agency, IBAMA.
The former minister defended his record on protecting the environment, saying he had sought to strike a balance between economic interests such as mining and agribusiness and the need to safeguard natural treasures like the Amazon.
He will be replaced by his secretary for the Amazon, Joaquim Alvaro Pereira Leite, he said.
Salles will probably be best remembered by his critics for an April 2020 cabinet meeting at which he was recorded saying the administration should use the coronavirus pandemic to relax environmental rules.
"Now that the media's only talking about Covid, we need to use this moment of calm to 'bring the whole herd of cattle through' and change all the regulations," he said.
He later denied he wanted to gut environmental protections, saying he meant only that the government should try to reduce red tape.
But activists and experts say he facilitated environmental destruction rather than fighting it.
The destruction of the Amazon, a vital resource for curbing climate change, has accelerated in Brazil since Bolsonaro and Salles took office in 2019.
Deforestation in the Brazilian Amazon surged by 85 percent in the administration's first year, destroying an area bigger than Puerto Rico, according to government data.
It has continued at a high rate since, last month setting a new record for May at 1,180 square kilometers (456 square miles) -- up 41 percent from the year before.
The Climate Observatory, a coalition of Brazilian environmental groups, reacted jubilantly to news of Salles's exit.
"Print this, put it on display and scream loud and clear in the streets: he fell!" it tweeted, along with a picture of Bolsonaro's official acceptance of Salles's resignation.
"Brazil simply could not continue to have someone in charge of the environment ministry who deliberately acted against the institution and was severely harming the country," environmental group Greenpeace said in a statement.
It cautioned, however, that it expected little change with Bolsonaro in power.
"Changing ministers is no guarantee that the Bolsonaro administration will change its destructive anti-environmental agenda," it said.
