In this work, we present an end‐to‐end solution for autonomous water sampling by utilizing an unmanned aerial vehicle (UAV) with a cable‐suspended mechanism. Towards this direction, a sampling mechanism is initially designed in such a manner that the water sampling success ratio is maximized. However, the disturbances, acting on the submerged mechanism due to the water flow during the sampling procedure, impede the stabilization of the vehicle above the desired sampling position. Consequently, to achieve the precise hovering of the UAV, the vehicle's sensor suite is further augmented with a load cell, a depth sensor, an ultrasonic sensor, and a camera. The respective measurements are appropriately fused by employing an extended Kalman filter (EKF). Hence, an estimate of the disturbances is available in real‐time and is incorporated into a Model Predictive Control scheme which compensates for the aforementioned disturbances and stabilizes the vehicle above the sampling location. Finally, a complete water sampling mission entails the safe and swing‐free transportation of the mechanism towards the sampling location and, then, to a position where the collected samples are postprocessed by human operators. Consequently, a model predictive controller is employed which ensures the navigation of the vehicle to the desired waypoints while minimizing the swinging motion of the mechanism. The state of the mechanism is obtained by fusing measurements provided by the load cell and the camera with an EKF. The performance of the proposed framework, which aims to address all the aspects of a water sampling mission, is demonstrated through real experiments with an octorotor.