[5] The lower, northwestern half of the river's watershed is a complex amalgam of glacial and tectonic features dating back to the Pleistocene, as well as more recent (Holocene) changes caused by a series of mudslides which flowed down from Mount Rainier between 5,600 and 800 years Before Present.

The upper watershed of the Puyallup River flows off of Mount Rainier through the South Cascade Range of Washington towards the lowlands surrounding Puget Sound.

It is characterized by deep glacial valleys carved through the low mountains and rugged foothills of Washington's South Cascade Range.

The main valley was originally part of a much larger lateral meltwater channel network formed during the Vashon Glaciation, which drained large portions of the Puget Sound Area as well as most of Washington's Cascade Range south into the Chehalis River prior to the unblocking of the Strait of Juan de Fuca around 14,800 years Before Present.

[11][12][13] As both sea level and land level recovered from the glaciation, the valley flooded and became a saltwater embayment of Puget Sound which extended through the Puyallup and Duwamish Valleys from Kenmore, Washington, on what is now Lake Washington, to Orting at the foothills of the Cascade Range.

The thick sediment deposits in the stream beds lower water capacity, which causes the river to meander and flood during periods of high streamflow.

In addition, the glaciers delay the onset of spring-summer runoff, compared to unglaciated river basins.

[5] Historically, these factors resulted in frequent flooding and extensive floodplain wetlands, and provided a rich and complex habitat for fish and other animals.

In addition, the river's mouth at Commencement Bay occupied an extensive tidal flat and wetland estuary delta.

Urbanization and an extensive system of flood control structures such as dams, levees, and culverts, have radically altered much of the Puyallup River and its tributaries.

The estuary delta at the mouth of the Puyallup River has been almost completely replaced with the facilities of the Port of Tacoma, with less than 5% of the original estuarine habitat remaining.

His legal case continued for years and resulted in the 1974 Boldt Decision, which granted half of all fishing rights in Washington state to native tribes.