Before the Protestant Reformation, the word pulpit was used for the platform on which the altar stood. It comes from the Latin word pulpitum, which means exactly that – a raised platform.
The Protestant Reformation brought a much more preaching-centric worship style, and since the speakers would often preach for extensive amounts of time, a lectern (literally, “a reading place”) was added to the pulpit to hold the Bible (since printed Bibles were often massive).
Remember that the primary movers and shakers of the Reformation (Luther, Calvin, Zwingli) were academics as well as pastors. In fact, you might say they were academics who collected salaries as pastors. The religious demands of priests and ministers in those days were minimal and most pursued other interests most of the time.
When these academics took to preaching, they brought their academic style of presentation with them. The distinction between the altar, meant for the observance of the Lord’s Table, and the pulpit where the preacher held forth became blurry. In time, the lectern itself began to be referred to as the pulpit and the altar was all but forgotten in most Protestant church buildings.
The pulpit originally served the practical function of holding the church’s copy of the Bible; but as printed Bibles became readily available, it became a place to put the preacher’s Bible. Eventually, it became a place to put notes, cups of water, and whatever else a preacher might store there.