The official state news service Agencia Brasil said about 100 city employees working full-time cleared nearly 80 tons of fish as of Sunday (local time). There was no immediate estimate of how many died, but several species were involved.
Rio's environmental secretary speculated that increased levels of a harmful algae may be the immediate cause of the sudden die-off Friday.
She told Globo's G1 website that authorities were still investigating, but the problem was not affecting the fish anymore.
The smell of rotting fish dampened runners' and cyclists' usual enthusiasm for leisurely jaunts along the Rodrigo de Freitas lagoon's paths.
The 4.5-square-kilometre body of water is just north of Rio's Ipanema Beach. A canal connects it to the Atlantic.