The Bayou Pierre site originally consisted of three earthen mounds. A fourth mound located roughly half a mile southwest of these mounds may also have been part of the site. All four mounds are included on a map drawn by Mississippi State Geologist B.L.C. Wailes in 1852.

Mound A is the only mound currently visible from Old Mill Road. It is a pyramidal platform mound approximately 16 feet in height. Archaeological excavations in 2013 determined that Native Americans built the mound in multiple stages during the Coles Creek period, from AD 1000-1200, but that it continued to be used until about AD 1350. They found evidence of activities on the mound summit, including fragments of pottery and stone tools that were discarded over the edge. However, there is no direct evidence for buildings, so it is unclear if the debris is related to a permanent residence on top of the mound or to more intermittent activities. While later Mississippi Period (AD 1200-1600) platform mounds had residences of chiefs on their summits, archaeologists are still debating whether Coles Creek mounds were used in this way.

Mound B is located about 90 feet north of Mound A and is currently visible only as a slight rise, while Mound C was destroyed by road construction in 1978. Excavations in the former location of Mound B indicate that its construction was contemporaneous with Mound A. However, stone artifacts recovered from beneath Mound B suggest a much earlier Archaic or Paleoindian occupation of the terrace on which the mounds were later constructed.

Mound D, half a mile away, was also built during the Coles Creek period, though pottery fragments indicate that the location may have been settled even earlier. Mound D was constructed in three distinct stages using basket-loaded fill as well as sod blocks for construction material. These mound building methods are evidence of a sophisticated understanding of how to engineer earthen monuments and are also in evidence at nearby sites such as Foster Mounds.