Water-related diseases remain the leading cause of morbidity and mortality, particularly affecting children in developing countries. Livestock grazing increases risk of waterborne pathogen contamination and related recreational diseases. This cross-sectional study clarifies the link between waterborne pathogens and cattle grazing practices in California’s Sierra Nevada. Range cattle feces and creek water samples around Lake Davis in Plumas County were collected to detect Salmonella, E. coli O157H:7, Cryptosporidium, Giardia and fecal indicator bacteria during the 2011 summer grazing season. Neither Salmonella nor E. coli O157H:7 were found in fecal and water samples. Cryptosporidium and Giardia loads (adjusted for percent recovery) in meadow creek water ranged from 0-2.8 oocysts/L and 0-2.3 cysts/L, respectively. Waterborne protozoa were found in both grazing and non-grazing areas, suggesting non-bovine sources exist in this watershed. Sequence analyses confirmed C. parvum and possible mixed concentrations of G. intestinalis assemblages B and C. Based on these water volume concentrations, ingestion of 3.6-9.1 and 4.3-14.3 L of creek water yields a 50% infection probability, assuming that all (oo)cysts are pathogenic and infectious. Overall prevalence of Giardia and Cryptosporidium in range cattle at this site was 19.5% (8/41) and 2.4% (1/41), respectively. Percentages of Giardia positivity were 60% (3/5) and 14% (5/36) with excretion intensities of 6,169 cysts/g and 42,694 cysts/g of feces in calves and adults, respectively. Calves had 4.3 times higher risk of yielding a positive test result for Giardia than were adults (95% CI 1.31-14.21; P = 0.04). Genotyping of positive feces revealed C. andersoni and G. intestinalis assemblage E. Because Cryptosporidium and Giardia found in creek water and cattle feces were different assemblages, the source of protozoa was unlikely to be cattle, and no association was found between fresh bovine fecal loads and concentration of waterborne protozoa.