The Sudd in South Sudan, formed by the White Nile’s Baḥr al-Jabal section, is one of the largest and most important wetlands in the world. Communities in the region almost exclusively depend on fisheries for food and livelihoods. Although threatened by over-exploitation and habitat changes, fish populations are also affected by climate change. Using semi-structured questionnaires, we assessed fisherfolk’s opinions of how recent variation in climate affected their livelihoods and the environment. Fisherfolk perceived that climate had changed in the past decade and were negatively impacted by this. Interviewees reported average higher temperatures, a greater frequency of floods and droughts, unpredictable timing of seasons, and erratic rainfall. Destruction of fishing villages/camps, loss and damage of fishing equipment, shifts in the fishing calendar, reduction of fish trade, and fish catch declines as well as psycho-social problems were given as the major consequences of climate change. Causes of climate change and variability were perceived to be linked to uncontrolled harvest of forest resources, anger of God and ancestors, and natural variability in climate. Most respondents expressed a desire to adopt more responsible behavior such as planting trees and establishing community nurseries, being educated on climate change risks, and sustainable fisheries management. Our results show that fisherfolk in the Sudd are troubled by climate change impacts on their livelihoods and on fish populations. In South Sudan, climate change has been reported from hydroclimatological data but concrete impacts on people remain largely unknown and of little concern because of recent wars and the poor economy. Our study provides an example of how fisherfolks’ local ecological knowledge (LEK) can be used as an early warning system of the negative impacts on livelihoods and fish populations and support adaptation to the changing climate. Supplementary Information The online version contains supplementary material available at 10.1007/s10113-022-01928-w.