Background: This study aimed to conduct a detailed and comparative analysis of body composition and dietary habits in elite swimming and water polo athletes. Through the examination of these key parameters, this study seeks to compare the dietary intake of these two distinct aquatic sports disciplines. Methods: A total of 10 top-level swimmers and 13 water polo athletes participated in anthropometric and body composition assessments, as well as a detailed analysis of nutritional intake. To compare the two groups, an independent samples t-test was used, and variance homogeneity was checked using Levene’s test. The effect size of the group differences was evaluated using Hedges’ g. Results: Water polo athletes showed significantly greater height (189.4 ± 2.9 vs. 186.5 ± 2.0 cm, p = 0.013), body mass index (24.3 ± 1.4 vs. 22.1 ± 0.5 kg/m2, p < 0.001), fat-free mass (62.9 ± 1.4 vs. 61.1 ± 1.38 kg, p < 0.001), skeletal muscle mass (47.1 ± 1.3 vs. 43.9 ± 1.6 kg, p < 0.001), and overall weight (86.9 ± 6.9 vs. 76.7 ± 2.2 kg, p < 0.001) in comparison to swimmers. Swimmers consumed greater amounts of mean daily energy (60.0 ± 1.0 vs. 39.0 ± 1.0 kcal/kg, p < 0.001), carbohydrate (7.8 ± 0.3 vs. 4.4 ± 0.5 g/kg, p < 0.001), protein (1.7 ± 0.5 vs. 1.4 ± 0.5 g/kg, p < 0.001), and fat (2.4 ± 0.5 vs. 1.7 ± 0.5 g/kg, p < 0.001) compared to water polo athletes. Conclusion: Our findings highlight the need for differentiated targeted nutritional interventions to enhance athletic performance in different types of water sports. Compared to water polo athletes, swimmers consumed significantly higher amounts of calories, matching their increased calorie demand from their specific training regime. However, this is an observational study and the differential needs of energy and macronutrients in water sports should be confirmed by studies with energy expenditure measurements.