Marcos Orellana, the UN Special Rapporteur on toxics and human rights, also expressed shock that children had died because of poor controls on pesticides, and called for better regulation.
Landfill sites and polluting industries in South Africa are often positioned in poor and migrant communities, Orellana noted in a statement.
Unemployment, hazardous synthetic chemicals and structural inequality were also among the reasons that make it difficult to overcome "the legacy of environmental racism", he added.
The country has "a landscape scarred by abandoned mines and tailing dumps and acid mine drainage", he added -- placed there during the apartheid era.
"The legacy of pervasive air, water and chemical pollution disproportionately impacts marginalised and poor communities," said Orellana, who on Friday concluded a 12-day visit to southern African nation.
And despite the new constitution's commitment to human rights, apartheid-era laws were still hampering progress.
"There are laws predating 1994 that continue to result in harms and human rights infringements, such as the laws governing hazardous waste from 1973 and pesticides from 1947," he noted.
He was "appalled" to learn that many children had died as a result of consuming or handling hazardous pesticides meant for agricultural use -- but sold illegally to combat pest infestations.
He called for accountability, warning that this could "begin to erode" the country's confidence in democracy if not remedied.
Mining, one of South Africa's largest industries, has left a legacy of thousands of waste dumps.
"The hope for pollution prevention and remediation upon mine closures is lost in the poor enforcement of legislation," Orellana said in his statement.
Coal mines in particular, have a severely negative impact on the air pollution in these communities, because of mercury emissions, ashes and dust.
Coal is a bedrock of South Africa's economy, employing almost 100,000 people and accounting for 80 percent of electricity production.
The country's environmental ministry welcomed the report, acknowledging that "rapid urbanization, industrialization and immigration, combined with fiscal challenges" had hampered efforts to tackle environmental challenges.
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