Relevant properties of the somatotype as important indicators can be associated with the body composition characteristics as well as both metabolic and bio-mechanical efficiency of athletes in the sport concerned. The primary aim of this single cross-sectional study was to determine the somatotype profiles in association with body composition and nutritional profiles among Lithuanian elite athletes (n = 189) involved in water, cycling and combat sports. The body composition along with the somatotype profiles and the nutritional status of athletes were evaluated using a battery of multiple frequency (5, 50, 250, 550, and 1000 kHz) bioelectrical impedance analysis (BIA) and a 3-day food record analysis. In terms of the prediction for athletes to be classified as endomorphs, mesomorphs or ectomorphs, the linear discriminant analysis was conducted to assess the grouping of samples. Both the multiple linear regression and multivariate logistic regression statistical analyses were performed to explore the associations between the independent and dependent variables. The central tendency values for the somatotype components of endomorphy, mesomorphy and ectomorphy in athletes playing water, cycling and combat sports were 4.3–4.9–3.4, 4.3–4.8–3.4 and 4.5–5.5–2.9, respectively. The central mesomorph somatotype with a trend towards endomorphy was dominant and varied according to a high muscle-to-fat ratio in elite athletes. Significant (p ≤ 0.001) positive associations between both endomorphy and mesomorphy values and higher body fat percentage as well as lower and upper limb muscle mass were identified. The lower levels of trunk muscle mass were related to athletes’ endomorphy and mesomorphy, too. Furthermore, in the athletes’ sample under analysis, high-level mesomorphs were prone to consume low-carbohydrate (adjusted odd ratio (AOR) 0.5, 95% confidence interval (CI) 0.2; 0.9) and high-protein diets (AOR 2.5, 95% CI 1.1; 5.5). Contrastingly, the elite athletes with a higher expression of endomorphy were on high-carbohydrate (AOR 5.4, 95% CI 1.1; 8.3) and high-fat diets (AOR 4.6, 95% CI 1.5; 7.1) along with insufficient protein diet (AOR 0.3, 95% CI 0.1; 0.9). Finally, whilst nutrition goals as a mediator can play a significant role in undergoing the maintenance of balance between the optimal body composition for athletic performance and the development of an ecto-mesomorphic somatotype, the elite athletes with higher levels of endomorphy value should be aware of lowering the body fat percentage coupled with dietary fat reduction and higher protein intakes. The findings obtained from the study may serve as an antecedent for a more targeted management of the elite athletes’ training process. Somatotyping as an additional assessment method can be successfully deployed in choosing correct coaching techniques, contributing to talent recognition processes or identifying reference morphometric parameters in elite athletes competing in water, cycling and combat sports.