Prepare your canning jars by washing them in hot, soapy water or running them through a dishwasher cycle. Keep them warm until ready to fill.
In a large mixing bowl, combine the sliced apples with the lemon juice, tossing to prevent browning.
In another bowl, whisk together the granulated sugar, brown sugar, flour, cinnamon, nutmeg, and salt.
In a large pot over medium heat, combine the apple mixture and sugar mixture. Add the water and mix well.
Cook the apple mixture on medium heat for about 10-15 minutes, stirring occasionally, until the apples are tender but not mushy. Remove from heat.
Using a canning funnel, carefully ladle the hot apple filling into the prepared jars, leaving about ½ inch of headspace at the top.
Wipe the rims of the jars with a clean cloth to remove any residue. Place the lids on top and screw on the bands until fingertip-tight.
In a water bath canner or large stockpot, bring enough water to a boil to cover the jars. Process the jars in boiling water for 20 minutes.
After processing, carefully remove the jars using the jar lifter and place them on a clean towel or cooling rack. Allow to cool completely for 24 hours.
Once cooled, check the seals: the lid should be concave and not pop when pressed. Store any unsealed jars in the fridge and use them within a few days.