The Petitcodiac River watershed features valleys, ridges, and rolling hills, and is home to a diverse population of terrestrial and aquatic species. Ten named tributaries join the river in its course toward its mouth in Shepody Bay. Before the construction of a causeway in 1968, the river had one of the world’s largest tidal bores, which ranged from 1 to 2 metres (3.3–6.6 ft) in height and moved at 5 to 13 kilometres per hour (3.1–8.1 mph). With the opening of the causeway gates in April 2010 and the complete replacement to a bridge in 2021, the river is flushing itself of ocean silts, and the bore is returning to its former size.

The section of the river that the PWA water quality sampling is performed at is located within the region of the Villages of Salisbury, Elgin and Petitcodiac, consisting of the area which drains into the headwaters of the Petitcodiac River system. This area is relatively rural, comprised mostly of forested areas, agriculture, forestry practices, and private dwellings. These streams flow into the Petitcodiac above the head of tide, which is the point to which the tidal bore influences the freshwater flowing down the river. This area has several rivers in comparison to the other areas of the watershed, and the waters are generally in good condition.