There are three ideas we need to deal with: absorbance, transmittance, and reflection. (good starting point here.) Let's think of fluids approaching a strainer.
Absorabance is a measurement of how much the strainer will capture and hold (light won't pass through it, but it won't reflect off of it, either).
Transmittance is a measurement of how well the strainer lets things pass (light passes through the material without stopping).
Reflection is a measurement of how well stuff will bounce off the strainer (light bounces off the material).
I'm also fond of the cherry analogy. Somebody throws a cherry at you. Did you duck, letting the cherry pass by (transmittance), catch the cherry in your mouth and swallow (absorbance), or catch it and spit out the seed (reflection)? Don't laugh, metaphors are rarely perfect.
Simplistically, water and glass have high transittance, low absorbance, and little reflection when looked at straight on. (Change your angle of view, though... now all the physics about light transitioning between mediums kicks in).
A common green leaf has high absorbance of red wavelengths, high reflectance of blue and green wavelengths, and low to no transmittance. Which means you see green, don't see red, and the ground beneath the leaf is dark.
Water's absorbance of IR is very good
Water aborbs IR. No reflection, no IR on the bottom of the pool, it's opaque.
Before I continue, remember to separate "how we see it" from "how it would be seen." We "see" the green reflected from a leaf, so it looks opaque (and green). We don't see the red absorbed by the leaf so it's "invisible" (meaning, it doesn't look red, if only looking in the red spectrum, it would look black).
It's helpful when dealing with aliens to think of what they "see" in their spectrum being symbolically identical to what we "see" in our spectrum. The short wavelength is blue, the medium wavelength is green, the long wavelength is red. They would symbolically (or perceptually) have the same kind of differentiation. What we'd call red they'd call blue and what we can't see they'd call red.
Why is this important? If you chase that "water absorbs IR" link you'll see that the deeper you go into IR, the less absorbant and more transmittant water becomes.
Which means, to a denizen of Titan (I believe there's enough of the IR spectrum there to do this, correct me if I'm wrong), a gently undulating surface of water would look remarkably like a lake full of low viscosity tar or oil would to us — black with bright reflections at the longer wavelengths.
As for the atmosphere, depending on what's actually in it (good point DarthDonut), they might see fog were we see clearly. They'll see clouds just like we do, but what's causing the clouds is a very different matter.