Little is known on the relationship between obesity and hydration level in children. To explore the possible association between children’s hydration status and body composition, we conducted this cross-sectional study. The survey was carried out in 2018 in Preliminary and High Schools from the Malopolska Province, Poland. The study group consisted of 264 children aged 7–15 years. The level of hydration was assessed based on urine osmolality during a school day. The examined had anthropometric tests and body composition assessment (FM, BF%, FFM, TBW, TBW%). Odds ratio (OR) and 95% confidence interval (CI) were calculated using a logistic regression analysis. In the study group, 9.5% of the examined were overweight, 7.2% obese, and it referred more to the country than towns (p < 0.05). Improper hydration was found in 53% of children, and 16.3% of them were severely dehydrated during a school day (urine osmolality > 1000 mOsm/kgH₂O). The level of dehydration was higher in children with excessive body fat (BF%) than in children with normal BF% [903.00 vs. 775 mOsm/kgH₂O]. Older age (>10 y) showed inverse association with dehydration [OR 0.52 (95% CI; 0.28–0.99)] and excessed BF% showed 2.3-fold increase in odds of dehydration during a school day [OR 2.39 (95% CI; 1.15–4.94)]. Improper hydration was a risk factor of difficulties with concentration declared by students during a school day OR 2.85 (95% CI; 1.16–6.99). Attention should be paid to appropriate hydration especially in children with excessive body fat content who feature a higher risk of dehydration and fluid demand.