Grand Canyon's tributaries all have the same following characteristics: hardness, high alkalinities (or buffering capacity), pHs around 8.5 (except for some of the warmer springs where pH is around 7.5) and dissolved oxygen levels in the range of healthy streams. Chemically, the tributaries can be roughly broken into two categories: those with high amounts of total dissolved solids (TDS) and those with low amounts of total dissolved solids. High TDS streams generally emerge from the lower carbonate strata. These streams include the Little Colorado River (LCR), and National, Kanab, Matkatamiba, Crystal, Warm Springs, Havasu, Spring Canyon, Kwagunt, Royal Arch, Hermit, Three Springs, and Nankoweap creeks. It is recommended that hikers avoid any water with high TDS, since these constituents cannot be removed through filtration.

Grand Canyon's water quality varies greatly when it comes to bacteria. Most of the tributaries have high bacterial counts some of the time. This bacteria may not be of human origin, but it does not have to be to cause illnesses. Animals can carry pathogens just as well as humans. Any stream exhibiting high fecal coliform or fecal streptococcus counts may also carry giardia as well. All water should be treated, filtered if possible, before consumption. Even tributaries running clear should be filtered because the simple act of filling a water bottle can stir up the sediments that are obviously the culprit to holding bacteria. Care should be taken during heavy use/water play so as not to ingest water, and one should consider any significant open wounds before entering.

Streams where radionuclides have been found include the LCR, the Paria River, Havasu, Kanab and Lava Chuar creeks, and Pumpkin Springs. The Paria River, Lava Chuar Creek and Pumpkin Springs have also tested higher in concentrations of arsenic, chromium, lead, zinc, copper, cadium, nickel, and beryllium than other waters. Drinking and bathing in these waters is not advisable.