Dehydration, assessed by urine and blood evaluation, is a risk factor for chronic kidney disease (CKD). The association between water deficit, as determined by a dietary assessment, and CKD prevalence is unclear. Therefore, this study aimed to clarify this association among adults in the USA. This cross-sectional study included the data of 9332 participants aged 18 years or older from the 2009–2012 National Health and Nutrition Examination Survey. Water turnover was calculated using an equation developed by the International Doubly Labelled Water Database Group. Total water intake was assessed by 24-h dietary recall on ≥ 1 d. Water deficit was defined as the ratio of water intake to water turnover. CKD was defined as an estimated glomerular filtration rate < 60 ml/min/1·73 m2, calculated by the 2021 CKD Epidemiology formula. OR for CKD prevalence were calculated using multivariate logistic regression and restricted cubic spline models. The mean daily water intake, turnover and deficit were 2799 ml, 3290 ml and –15 %, respectively. CKD prevalence was 6·3 %. After adjusting for lifestyle and urine and serum osmolality, the fourth water deficit quartile was inversely associated with CKD prevalence when compared with the first quartile (OR, 0·71; 95 % CI, 0·51, 0·98). In the spline analysis, the water deficit at which the OR for CKD prevalence plateaued was approximately –30 % to 0 %. Water deficit had an L-shaped association with CKD prevalence independent of urine and serum osmolality, highlighting the importance of assessing water intake relative to dietary needs. These findings may assist the development of water requirements.