Place the carrots, onion and water in a blender and puree. Add the mangoes and puree until smooth. Carefully, adding one at a time, blend in the habaneros for one more minute until smooth.
Pour the mixture into a large saucepan, add the vinegar, agave syrup and salt. Bring to a boil, reduce heat to low, cover partially with a lid and simmer until the sauce coats the back of a wooden spoon, about 30 minutes. Stir every 8 to 10 minutes to make sure doesn't stick to the bottom of the pan.