Due to siltation, the river is only fully accessible to motorized boats west of the Durham Water Plant for approximately three hours on either side of high tide.

[citation needed] The Oyster River valley, like the rest of New England, was entirely covered by ice during the last continental glaciation.

As forests diminished, soil usually held in place by tree roots started to wash into the river, causing its waters to fill with silt.

The Oyster River community was one of the three original Dover settlements, which also included Hilton Point and the current Durham town center.

[6] In November 2020, consultants with Vanasse Hangen Brustlin, Inc. (VHB) advised that the dam should either be removed or stabilized, and that taking no action would leave "the community at risk for a future safety issue.”[7] A news report in January 2021 cited cost estimates of $4 million for stabilization vs. $1.3 million for removal.

These floodplain areas are useful in holding excess water during severe weather and help to reduce the damage done to the infrastructure elsewhere along the river.

Due to siltation and water pollution in the river, the population of oysters hit an all-time low in 2000 at 6,174 US bushels (217,600 L).