Conety Run begins on Stony Cabin Ridge in Fairview Township. It flows west for a short distance before turning south-southwest for several tenths of a mile. It then passes through Fountain Lake and turns south for several tenths of a mile. The stream then enters Dennison Township and turns south-southeast. After more than a mile, it turns south-southwest and then south, crossing Pennsylvania Route 437. The stream then flows south-southeast for several tenths of a mile until it reaches its confluence with Little Nescopeck Creek. Conety Run joins Little Nescopeck Creek upstream of its mouth.
Hydrology
Conety Run is not considered to be impaired. The concentration of alkalinity in Conety Run is 2 milligrams per liter. The stream is slightly acidic, with a pH of 6.2. The concentration of water hardness is 5 milligrams per liter. The specific conductance of the waters of Conety Run is 22 micro-siemens.
Geography and geology
The elevation near the mouth of Conety Run is above sea level. The elevation near the stream's source is between above sea level. The surficial geology along the lower reaches of Conety Run mainly consists of alluvium. However, bedrock consisting of sandstone and shale, a glacial or resedimented till known as Wisconsinan Till, and a small patch of Wisconsinan Ice-Contact Stratified Drift are also present in the stream's vicinity. In the stream's upper reaches, the surficial geology consists almost entirely of bedrock and Wisconsinan Till.
Watershed
The watershed of Conety Run has an area of. The mouth of the stream is in the United States Geological Survey quadrangle of White Haven. However, its source is in the quadrangle of Wilkes-Barre East. The watershed is in the northwestern part of the Nescopeck Creek watershed. The watershed is considerably longer than it is wide. Considerably more than 80 percent of the watershed of Conety Run is forested land. There are fewer than of local roads in the watershed of Conety Run. There are only a few miles of state roads in the watershed. Pennsylvania Route 437 is in the vicinity of the stream. A lake known as Fountain Lake is located near the headwaters of Conety Run.
Conety Run is considered by the Pennsylvania Fish and Boat Commission to be Class A Wild Trout Waters for brook trout from its headwaters downstream to its mouth. It has held this status since at least 2012. However, the stream is considered to be infertile. Fish were stocked in Conety Run in the early 1960s.