[5] The Portneuf River was given its name sometime before 1821 by French Canadian voyageurs working for the Montreal-based fur trading North West Company.

Nutrient runoffs from intensive agriculture and ranching along the route of the river have noticeably increased the nitrate loads in the stream.

This is compounded by the addition of treated effluent from the city of Pocatello's wastewater treatment facility and the waste associated with the phosphate processing plant, Simplot.

[10] The DEQ in collaboration with the City of Pocatello, the Soil Conservation Commission, and USDA are developing tools and practices designed specifically to alleviate the nitrogen issues associated with agriculture and its waste.

Known as Best Management Practices (BMPs), these methodologies are designed and modified for varying situations and have proven themselves effective through prior implementation projects.

[10][15] Enrichment of CaCO3 in the meteoric waters is due to the addition of CO2 either through interaction with the atmosphere, or infiltrating through organic compound containing soil layers.

This is a phenomenon noticed throughout the world as the development of waterfall tufa[16] and is a relevant explanation for at least some formation through the region, especially through the town site of Lava Hot Springs.

Algae and mosses, along with higher plants and some insects, often trap tiny particles within their sinuous roots, fronds, and shelter/feeding structures, acting as nucleation points for further precipitation.

[16] This may explain some of the deposition locations, but the biota plays a larger role as photosynthetic plants remove CO2 from the water, further concentrating the Ca2+ and CO32− and driving precipitation.

The Portneuf through this reach is rich in plant life not only due to the nutrient accumulation as it travels through farmland but from the warm water inputs that protect the stream from the effects of the harsh cold of winter temperatures.

An interesting study completed in 1972 showed evidence that the development of tufa and travertine filled the interstices normally found on the rocky river.

[10] Precipitation of tufa in the Portneuf drainage is produced through the combination of four complex mechanisms: dissolution of limestones by meteoric waters containing carbonic acids, degassing of CO2 at turbulent sites, the removal of CO2 by photosynthetic plants, and the trapping of particles of CaCO3 by the biota.