The invention of the reel was a crucial development as far as salmon fishing was concerned and if you would like to read more about that, we would suggest taking a look at this page. But trout fishermen continued to use short (six foot) rods with fixed horsehair lines, as well as longer 'loop' rods (up to sixteen feet long, with a running line that passed through a loop at the top) right into the early years of the 18th century. Their flies were fished close enough to the top that they could literally dangle them in the surface layer, which is where most of the takes occurred and they fished upstream or down depending on which way the wind blew.
During the 18th century, use of the reel became widespread and the use of the short rod became less common, until by the beginning of the 19th century it was quite unusual to see a trout fisherman with a rod much shorter than 11 or 12 feet. Pure horsehair lines gradually gave way to mixed silk/horsehair, which in turn was replaced by braided silk lines from about the second quarter of the 19th century. The problem with the longer braided silk lines was that they sank and this, together with the lack of stiff rods encouraged most trout fishers to fish downstream - and the technique that we know as the wet fly was born.