During the 2012–2016 drought in La Guajira, Colombia, child mortality rates rose to 23.4 out of 1000. Most of these children belonged to the Wayuu indigenous community, the largest and one of the most vulnerable in Colombia. At the municipal level, this study found a significant positive correlation between the average child mortality rate and households with a monthly income of less than USD 100, the number of people without access to health insurance, being part of the indigenous population, being illiterate, lacking sewage systems, living in rural areas, and large households with members younger than 5 years old and older than 65 years old. No correlation was found with households without access to a water source. The stepwise regression analysis showed that households with a monthly income of less than USD 100, no members older than 65 years old, but several children younger than 5 years old, account for 90.4% of the child mortality rate. This study concludes that, if inhabitants had had better incomes or assets, as well as an adequate infrastructure, they could have faced the drought without the observed increase in child mortality.