Water quality assessment programs for the management of water resources require the collection of water samples for physical, chemical, and biological analyses. Lack of personnel, accessibility of water bodies, and time constraints, especially after natural disasters and emergencies, are some of the challenges of water sampling. To overcome these challenges, a custom-made thief-style water sampling mechanism was developed and mounted on a multirotor unmanned aerial vehicle (UAV) for autonomous water sampling. The payload capacity and endurance of the UAV were determined using an indoor test station. The UAV was equipped with floatation, and electronic components were coated to prevent water damage in the event of a forced landing or for sample collection. Water samples from a 1.1 ha pond were collected with the developed UAV-assisted water sampling system and traditional manual methods. Dissolved oxygen (DO), electrical conductivity (EC), pH, temperature and chloride measurements were made on samples collected with both UAV-assisted and manual methods and compared. Percent differences between the two sampling methods for DO, EC, pH, and temperature were minimal except for chloride level. Percent differences between the two sampling methods for DO, EC, pH, and temperature measurements were 3.6%, 2.3%, 0.76%, and 0.03%, respectively. Measured chloride levels for the manual and UAV-assisted sampling methods were 3.97 and 5.46 mg/L. UAV-assisted water sampling may prove faster and safer than manual water sampling from large surface waters and from difficult to access water bodies.