The integration of the methodological basis of several different sciences in interdisciplinary research is a characteristic feature of new mechanisms for solving modern applied problems. The emerging theoretical foundations of aerolimnology, as a new scientific direction, are considered from the point of view of the contribution of three key sciences to it: limnology, informatics and robotics. Classifications of methods and approaches of limnological research, airborne robotic means, and information technologies that are promising for solving problems in the field of aerolimnology are given. The task of the scientific direction of aerolimnology is formulated as the study of the possibilities and limitations of combined methods of remote sensory measurement, robotic sampling and analytical study of the parameters of freshwater ecosystems to monitor and predict the dynamics of their development. Among the main areas of aerolimnological research, the following are distinguished: the construction of orthophotomaps and photogrammetric spatial models of the bottom topography and individual elements of the bottom landscape and coastal zone of various scales; geological and geophysical mapping of the underwater part of the coastal zone; the study of phytoplankton, in particular, the "bloom" of water caused by cyanobacteria; study of distribution and migration of large representatives of hydrofauna; study of temperature fields and processes of redistribution of water masses. The limitations imposed on the use of unmanned aerial vehicles (UAVs) in sampling and monitoring coastal water areas are discussed, primarily weather-climatic, temporal, spatial, and technical. The advantage of using unmanned aerial vehicles in aerolimnology is justified by an increase in the speed of data acquisition, the possibility of approaching hard-to-reach and territorially remote objects, and a decrease in the influence of the human factor. The scientific novelty of the presented research consists in an attempt to integrate interdisciplinary knowledge when using unmanned aerial vehicles and processing the obtained data based on artificial intelligence technologies in the study of limnological objects and processes. The important role of geoinformation systems is noted and examples of maps of shore typification and geomorphology of Lake Ladoga are given, posted on the website of the Center for the Collective Use of Scientific Equipment "North-Western Center for Monitoring and Forecasting the Development of Territories" of the St. Petersburg Federal Research Center of the Russian Academy of Sciences. The main stages of the methodology for conducting aerolimnological studies using interdisciplinary approaches based on limnology, informatics and robotic tools operating in different environments are considered.