filter it
if you still have concerns:
boil some water, add salt to the water to raise its boiling point
if properly capped they should be waterproof, drop them into the water and boil for 20-40 minutes
this will kill anything living that may be in them (i say living cause contaminants are not alive and dont 'die') - thats what the filter is for
the filter also removes bacteria as they are physically too large to pass through it