Yep! See several entries in http://amasci.com/brain/ for tricks to try with this.
The effect is well known to physics teachers. It goes by the name “Hot Chocolate Effect”, since people often notice it while stirring cocoa powder into hot water. The millions of micro-bubbles carried by the powder alter the speed of underwater sound waves.
There’s a second error in Cecil’s answer. Yes, sound moves fast in liquids, and slower in gases, but it moves amazingly slowly in liquid/gas or solid/gas mixtures. The speed of sound is extremely slow in bubble-containing liquids, in foams, and in fluidized sand beds. “Moaning sand dunes” and “squeaking sands” get their pitch from the same physics.
As I understand it, the speed of wave propagation is proportional to the density and also to the rigidity of the material, with high density giving slower sound and high rigidity speeding it up. Solids are dense (slow sound) but rigid (fast sound), while gases are less dense (fast sound) but very springy (slow sound.) So, in liquids and and in gases the two effects fight each other. To REALLY slow down the sound waves requires a very springy, very dense material: Liquids with bubbles, or extremely dense fog or dust.
A fairly tiny patch of underwater bubbles can acts as an “acoustically large” chamber, behaving as a low-freq resonant cavity. As the cloud of underwater bubbles rises, the cavity gets smaller and its resonance frequency rises. Which leads to a prediction:
STIR THE COFFEE WELL AND THE FREQUENCY GETS LOW AGAIN! (Try it, it works! Well, it works if you stir it just before the cloud of microbubbles actually reaches the surface. Or you can stir-and-clink constantly, and the pitch will descend. Clink-without-stirring and the pitch ascends.)
I’ve noticed this pitch-change with hot water fresh from the tap. As before, it’s from a cloud of invisibly small bubbles. If you put a tiny bit of dish soap into the hot water, it keeps the bubbles from popping when they reach the surface, so you can see the tiny bit of froth that eventually appears. The froth is the remenants of the bubble-cloud which caused all the weirdness.
In coffee, the bubbles usually come from the dissolving sugar (or the instant coffee powder.) The grains aren’t instantly “wetted” by the water, so each grain carries a layer of air. As the sugar wets and begins dissolving, the air layers turn into extremely tiny bubbles. You can detect the bubbles as before: mix sugar into cold water that has a bit of dish soap. After ten minutes or so, a thin layer of froth will become visible.
I hear deep thunking noises in the kitchen! They’re coming from the beaters as they hit the sides of the bowl full of meringue (or even whipped potatoes.) It also happens when you stir ice cream into root beer. The material in the container has become acoustically large. What can we use it for? Make a Willy Wonka portable tabletop pipe organ with foam-filled organ pipes which can play deep bass notes just like a full sized instrument. Wear laytex clothing, it could get messy.