The Nyakagunda River originates in the north of Cibitoke Province and flows west and then south to Nyeshenza.

From there is flows southwest and then south to Rugombo, forming the western boundary of that city, near its mouth on the Ruziz River.

[12] In January 2020 torrential rains caused the Nyakagunda River to deviate from its bed in the Commune of Rugombo and damage irrigation infrastructure and crops of rice and banana.

[14] In September 2023 seven out of seventeen collines in the Commune of Rugombo were experiencing water shortages.

People of these collines had to use dirty water from the Nyakagunda and Nyamagana rivers, which contain bacillary dysentery and cholera, as well as toxic run-off products from agriculture.