Water salinity is a growing global environmental health concern. However, little is known about the relation between water salinity and chronic health outcomes in non-coastal, lean populations. Daasanach pastoralists living in northern Kenya traditionally rely on milk, yet are experiencing socioecological changes and have expressed concerns about the saltiness of their drinking water. Therefore, this cross-sectional study conducted water quality analyses to examine how water salinity, along with lifestyle factors like milk intake, was associated with hypertension (blood pressure BP ≥140 mm Hg systolic or ≥90 mm Hg diastolic) and hyperdilute urine (urine specific gravity <1.003 g/mL, indicative of altered kidney function). We collected health biomarkers and survey data from 226 non-pregnant adults (46.9% male) aged 18+ from 134 households in 2019 along with participant observations in 2020. The salinity (total concentration of all dissolved salts) of reported drinking water from hand-dug wells in dry river beds, boreholes, and a pond ranged from 120 to 520 mg/L. Water from Lake Turkana and standpipes, which was only periodically used for consumption when no other drinking sources are available, ranged from 1100 to 2300 mg/L. Multiple logistic regression models with standard errors clustered on households indicate that each additional 100 mg/L of drinking water salinity was associated with 45% (95% CI: 1.09–1.93, P = 0.010) increased odds of hypertension and 33% (95% CI: 0.97–1.83, P = 0.075) increased odds of hyperdilute urine adjusted for confounders. Results were robust to multiple specifications of the models and sensitivity analyses. Daily milk consumption was associated with 61–63% (P < 0.01) lower odds of both outcomes. This considerable protective effect of milk intake may be due to the high potassium, magnesium, and calcium contents or the protective lifestyle considerations of moving with livestock. Our study results demonstrate that drinking water salinity may have critical health implications for blood pressure and kidney function even among lean, active pastoralists.