The River Brue originates in the southwestern hills, situated to the southwest of its catchment area near the Dorset border. These hills also serve as the source of the River Wylye and the Dorset Stour, which flow southward towards the English Channel. The river swiftly descends through a narrow valley, joining forces with the River Pitt just beyond Bruton. From this point, the river meanders through a broad, flat-bottomed valley that stretches between Castle Cary and Alhampton. As it reaches Baltonsborough, its elevation decreases to approximately 10 meters (33 ft) above sea level, and the surrounding countryside drains into it through numerous rhynes. Passing by Glastonbury, the river acts as a natural boundary with the nearby village of Street before traversing a predominantly man-made channel across the Somerset Levels and eventually merging into the River Parrett at Burnham-on-Sea. Along its course, the River Brue receives contributions from the North Drain, White's River (which carries the water of the River Sheppey), Cripps River (an artificial channel connecting it to the River Huntspill), and various drainage rhynes. Additionally, it connects with the River Axe through several controlled channels equipped with sluices. Tidal effects become evident below the sluices at New Clyce Bridge in Highbridge.
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The area surrounding the River Brue has been inhabited since the Neolithic era, during which people exploited the reedswamps for their natural resources and constructed wooden trackways such as the Sweet and Post Tracks. The Sweet Track, discovered in 1970 by a peat digger and dating back to the 3800s BC, holds the distinction of being the world's oldest timber trackway. In fact, it was once considered the oldest engineered roadway as well. The Sweet Track was built between an island at Westhay and a ridge of high ground near the River Brue, close to Shapwick, during the early 4th millennium BC. Similar track remnants have been unearthed in the vicinity, connecting settlements on the peat bog, including the Honeygore, Abbotts Way, Bells, Bakers, Westhay, and Nidons trackways.The Somerset Levels boast the best-preserved prehistoric village in the UK, known as Glastonbury Lake Village, along with two others at Meare Lake Village. Discovered in 1892 by Arthur Bulleid, Glastonbury Lake Village was home to approximately 200 individuals who lived in 14 roundhouses. The village was constructed on a marshy area, utilizing an artificial foundation made of timber filled with brushwood, bracken, rubble, and clay.During the Romano-British period, the valley played a significant role in salt extraction activities. At that time, the Brue formed a lake just south of the hilly terrain where Glastonbury stands. According to legend, this lake is one of the suggested locations for the home of the Lady of the Lake in Arthurian tales. Pomparles Bridge, positioned at the western end of this lake, served as a protective structure for Glastonbury from the south. It is believed that Sir Bedivere cast Excalibur into the waters near this bridge after King Arthur fell at the Battle of Camlann. Historical records from the 16th century by John Leland noted the bridge as having four arches, while an 1839 illustration by W. Phelps depicted it with only two arches—one pointed, likely from the 14th or 15th century, and the other round. Excavations conducted in 1912 revealed the remains of a second round arch, estimated to date back to the 12th century. The current concrete arch bridge was constructed in 1911 and later expanded in 1972. It serves as the passage for the A39 road over the River Brue.