The purpose of this study was to determine the association between social and environmental indicators and high mortality rates from chronic kidney disease (CKD) in municipalities of Guatemala. An ecological study of municipal-level factors associated with CKD mortality in Guatemala was conducted. Crude mortality rates were calculated for the 2009–2019 period for each of the country’s 340 municipalities, by gender and age groups. Municipal-level social and environmental indicators were used as independent variables. Linear regression was used for bivariate and multivariate analysis. A total of 28,723 deaths from CKD were documented for the 2009–2019 period. Average crude mortality rate for all ages for the country’s 340 municipalities was 70.66 per 100,000 [0–502.99]. Very highly positive associations with high mortality rates were found in two agrarian territories where land use is mainly for permanent crops (e.g., sugar cane, coffee, rubber, banana, plantain, African palm) and pastures for cattle, with very low percentages of land covered by forests or protected areas. Social factors related to poverty and environmental factors related to agricultural use of land may play a role in the high CKD mortality rates documented in a cluster of municipalities of Guatemala.