The Kinnel Water rises on the southern edge of the Lowther Hills around 2 kilometres (1.2 mi) north of the top of Queensberry near the border with the neighboring council area of South Lanarkshire. A source river flows from the River Clyde, which flows to the northwest, at a distance of around 400 m (1,300 ft). After its upper course mainly follows a south-eastern direction through a hilly landscape, its course takes a southern direction after about 2 kilometres (1.2 mi). For a few kilometers, the A701 runs largely parallel to the left bank before crossing the river. Around 2 kilometres (1.2 mi) northeast of Lochmaben it joins the River Annan, which subsequently flows into the Irish Sea via the Solway Firth. With a total length of around 32 km (20 mi), the river overcomes a height of 402 m (1,319 ft).[2][1]
Several streams flow into the Kinnel Water on its course; there are no significant inflows other than the Water of Ae that flows into Templand. The Kinnel Water runs through a sparsely populated region, so that it affects few towns, of which Templand is the most populous.