Whisk together all the ingredients for the pudding except the chia seeds in a large bowl.
Once fully incorporated, add the chia seeds and mix in. Cover with plastic wrap and refrigerate for at least 3 hours to overnight until a pudding/gel like consistency is achieved.
For the cranberry sauce
Bring the water and sugar to a boil in a small sauce pot.
Add the cranberries, cinnamon and nutmeg. Stir and lower the heat to a simmer.
Simmer, stirring often until the cranberries have broken down and most of the liquid cooked off, about 10-15 minutes. Turn off heat and let cool.
To assemble the the parfaits, alternate layers of cranberry sauce and chia pudding in glass jars or serving cups.