The Maine Department of Marine Resources manages this system for a commercial escapement of 35 fish per acre. The spawning escapement needs for this system are 20,000 river herring passed upstream by the harvester throughout the season. The management plan has always achieved returns to meet the target escapement developed for this system or passed the entire run upstream. Harvesting occurs in the fishway just downstream of Long Pond, which is the only accessible spawning habitat on the east branch of the Sheepscot River. The Department of Inland fisheries and Wildlife will not permit alewives access to historical spawning habitat in Sheepscot Pond, or the watershed above, because of concerns with disease issues that may effect sport fish raised at a state own fish hatchery on Sheepscot Pond.
The west branch of the Sheepscot River leading to Branch Pond contains very few river herring. For several years the DMR stocked Branch Pond to propagate an artificial run while planning and designing a fishway to provide access to Branch Pond. An old mill sits directly on top of the outlet stream and the engineering and constructions costs of installing fish passage at this time is prohibitive. Stocking Branch Pond no longer occurs but will resume if fisheries staff can overcome fiscal challenges to acquiring fish passage in the future. There are stray river herring that do ascend the west branch each year but the numbers are low and not harvested commercially. The commercial harvester, through the town of Alna, retains the right to harvest these fish. The harvester keeps the west branch closed to promote natural recolonization of blueback herring to this branch of the river.
Spawning habitat is available to blueback herring in the river below the fishway. Incidences of blueback herring in the commercial catches or sampling below the fishway are rare. There is no available spawning habitat for alewives in the Sheepscot River below the commercial fishery and there are no reports of juvenile blueback herring emigrating from this system in appreciable numbers.
The Sheepscot River alewife run would be considerably larger if all historic river herring habitat were accessible to river herring. Access restrictions placed on the harvester and the Maine Department of Marine Resources by the Maine Department of Inland Fisheries and Wildlife are unlikely to change in the near future.