Yup you don't want dwarves drinking muddy water. ramps block well access, and wells require at least 3/7 of water below them.
In order to ensure that wells don't dreg up . . . dreg you have to use water at least two deep. In short, aquifers alone aren't sufficient to provide wells without tampering.
Tampering may include pumping it out to make it deeper (if the aquifer is only one tile deep it should make a small infinite supply) collapsing a cork onto it, and perhaps collapsing the cork again for more depth (actually a favored method of mine, as I can just make the grand hall the above ground well-site. It looks good and functions), or wait for it to freeze. On fairly uneven ground or at the borders of biomes (or careful manipulation of ores) you can create a suitable location with caution.
http://dwarffortresswiki.org/index.php/DF2012:Aquifer#Dealing_with_aquifersIn general sandy aquifers make you hate life.
I would recommend you make a cistern of any groundwater or wait for winter in freezing biomes before trying to run a well to the aquifer, unless you feel okay making a cork. Also a thought, if you make a (large) cistern below the aquifer, you can put a barrier up and link it up and pierce it from below. Just as secure, if you don't mess up. But a mistake in the planning would mean infinite water pouring into you secure fortress.