Water sample collection is a simple, but fundamental approach for measuring water properties that cannot currently be sensed in situ with instruments or for conducting experiments requiring water samples. Conventional approaches to water sampling typically employ research vessels which are costly, limited by sea state, and are often restricted by scheduling and other logistics. These factors can limit the ability to sample transient phenomena in inland and coastal waters. They can also restrict sampling frequency for time series measurements. We describe the use of aerial drones and newly developed sampling bottles that allow sub-surface water collection without the use of research vessels. The sampling bottles are similar in operation to conventional Niskin bottles, but with the different methods for closing the bottles. We have experimented with two closing methods. One uses a float and mechanical linkage to close bottles at fixed depths and the other uses pressure sensors to close bottles at programmed depths. Drone-based water sampling is currently employed in the Santa Barbara Coastal Long Term Ecological Research (SBC LTER) project to obtain weekly time series of water samples for pH and total alkalinity at a long-term oceanographic mooring. The water samples are also being used to calibrate pH sensors on the mooring and assess data quality. Drone sampling will be expanded to other SBC LTER moorings in the future. Aerial drones offer a new approach for sampling the coastal ocean and inland waters. Drone-based sampling is in its infancy, but we envision the development of a suite of specialized instrumentation and water collection devices that take advantage of the capabilities of aerial drones. This will allow rapid response for sampling transient events such as harmful algal blooms and toxic spills in a wide range of environmental conditions.