The study conducted secondary analysis to identify hotspot clusters and seasonality trends of acute malnutrition. The team used data from 2010 to 2020, including global acute malnutrition (GAM) data from the Integrated Standardized Monitoring and Assessment of Relief and Transitions survey and middle- and upper-arm circumference data from the National Drought Management Authority sentinel surveillance sites. Levels of acute malnutrition were categorized according to the global Integrated Phase Classification (IPC) severity phase: acceptable (<5%); alert (5–9%); serious (10–14.9%); critical (15–29.9%); and extremely critical (≥30%). Both counties consistently experience high levels of acute malnutrition, even in non-drought years. The findings showed rates of GAM in Marsabit persistently above the critical threshold of ≥15%. In Isiolo, the findings revealed no years in which the prevalence of GAM was within the acceptable range (≤ 5%). In three of the 10 years, GAM rates exceeded the critical threshold of ≥ 15%, and for six years GAM was above the serious threshold. Hotspots were identified at the sub-county level in both counties, which informed the geographic focus areas for Nawiri Year 3 Phase 2 implementation.