Alice Kayitesi, the mayor of the southern Kamonyi district, confirmed the incident, which took place in the Nyabarongo river on Wednesday.
The victim’s name and age have not been made public yet.
“He had broken the stay-home rule, he’s among very few people here who are not cooperating with the lockdown to stop the virus,” Kayitesi told BBC news.
Rwanda’s government had urged citizens to stay at home from Sunday in a bid to curb the spread of Covid-19.
The country has recorded about 41 infections so far.
The East African nation has the highest number of cases in the region, even though no deaths have been recorded.
The country has declared unnecessary movement outside homes during the global pandemic illegal, except for essential services.