My boss tends to overuse the word "suppose". He'll say stuff like
I suppose you received my email?
Now, clearly there are more things wrong with that sentence than just using "suppose" in a context where "presume" or "assume" would be much more idiomatic: to start with, if he wanted to ask a question, he should have asked a question, instead of merely tacking on a question mark (or rather, the corresponding inflection, since this was spoken, not written) to the end of a statement. But let's just stick to word choice for now.
The dictionary definitions of presume, assume, and suppose make them seem pretty much interchangeable.
presume: to take for granted, assume, or suppose
suppose: to assume (something), as for the sake of argument or as part of a proposition or theory
assume: to take for granted or without proof: to assume that everyone wants peace. Synonyms: suppose, presuppose; postulate, posit.
But to my ear, suppose is the wrong word to use in most situations.
I suppose you are using Internet Explorer.
This is perfectly understandable — idiomatic, even, if delivered with the appropriate sneer — but to me, it means something quite different than
I assume you are using Internet Explorer.
However, I have been utterly unable to articulate what the difference is, at least not in a manner that gets my point across to my boss.
Best Answer
To suppose that something is true means to think that it is true, but to freely acknowledge that it may just as well be false. To assume that something is true means to act as if it were true, but with no implication that there is proof that it is. To presume that something is true is to base an assumption of truth on some sort of probability or evidence.
So, "I suppose you are using Internet Explorer" is a slightly weaker assertion than "I assume you are using Internet Explorer." For an example of presume: "One may presume that he is using Internet Explorer, because he is using Windows and is a computer novice."
These are not hard-and-fast rules; as you have seen the meanings overlap to some degree. This is especially true of suppose and assume.