Good water quality is important for the plants and animals of the riparian community. Fish, aquatic insects, amphibians, and perhaps endangered species could easily be affected by poor water quality. High bacteria counts have been observed in the park. In 1972, E. coli counts as high as 16,000 ppm contributed to a die off of several mammal species. The US Public Health Service identified the culprit as infection due to the bacterium genus Arizona (closely related to genus Salmonell a).
Riparian areas are the most heavily used by visitors and are where most structures are located. Human impact such as littering and human waste can adversely affect long reaches of stream. Routine limnological surveys of the park's surface waters are one potential monitoring solution. Aquatic insects and amphibians may also be utilized as indicator species of overall surface water quality.
Good water quality is also important for visitor and resident safety. The east side headquarters and residence area is serviced by a well that taps the valley alluvium near the east entrance. That source is reliable and recently replaced a well near the old Chalone Creek campground. The west side offices and residences are serviced by a deep artesian well that requires no pumping. Those sources are treated regularly to guard against public health threats. An analysis of an east side well in 1959 yielded chemical data on a domestic water well. That data showed that the water had a pH of 6.7, moderate hardness, specific conductance was 407, and contained 280 ppm of dissolved solids.