Accurate feeding management in aquaculture relies on assessing the average weight of aquatic animals during their growth stages. The traditional method involves using a labor-intensive approach and may impact the well-being of fish. The current research focuses on a unique way of estimating red tilapia’s weight in cage culture via a river, which employs unmanned aerial vehicle (UAV) and deep learning techniques. The described approach includes taking pictures by means of a UAV and then applying deep learning and machine learning algorithms to them, such as convolutional neural networks (CNNs), extreme gradient boosting (XGBoost), and a Hybrid CNN-XGBoost model. The results showed that the CNN model achieved its accuracy peak after 60 epochs, showing accuracy, precision, recall, and F1 score values of 0.748 ± 0.019, 0.750 ± 0.019, 0.740 ± 0.014, and 0.740 ± 0.019, respectively. The XGBoost reached its accuracy peak with 45 n_estimators, recording values of approximately 0.560 ± 0.000 for accuracy and 0.550 ± 0.000 for precision, recall, and F1. Regarding the Hybrid CNN-XGBoost model, it demonstrated its prediction accuracy using both 45 epochs and n_estimators. The accuracy value was around 0.760 ± 0.019, precision was 0.762 ± 0.019, recall was 0.754 ± 0.019, and F1 was 0.752 ± 0.019. The Hybrid CNN-XGBoost model demonstrated the highest accuracy compared to using standalone CNN and XGBoost models and could reduce the time required for weight estimation by around 11.81% compared to using the standalone CNN. Although the testing results may be lower than those from previous laboratory studies, this discrepancy is attributed to the real-world testing conditions in aquaculture settings, which involve uncontrollable factors. To enhance accuracy, we recommend increasing the sample size of images and extending the data collection period to cover one year. This approach allows for a comprehensive understanding of the seasonal effects on evaluation outcomes.