Areas near the Dien Bien Phu, Kieu and Hoang Hoa Tham bridges reported mass fish deaths.
Most of the dead fish are tilapia, catfish and carp. The fish were blanketed with rubbish.
Despite wearing masks, people passing the affected areas have struggled with the bad odour.
Nguyen Van Hung, a motorbike driver near Hoang Hoa Tham Bridge, said the fish deaths were visible in the canal for several days following heavy rain.
The severely polluted water runs through Tan Binh District and District 3.
Nhieu Loc-Thi Nghe Canal is 10 kilometres long, flowing through districts 1 and 3 and the districts of Binh Thanh, Phu Nhuan and Tan Binh and then into Saigon River.
The canal regularly experiences mass fish deaths at the beginning of the rainy season. The most severe incident happened in 2016 when environmental workers collected up to 70 tonnes of dead fish. Authorities in HCM City had to use tonnes of chemicals to clean the canal water.
