Approximately three-fourths of our planet’s surface is covered by ocean and seas, a continuous body of water that is divided into several oceans and smaller seas. Water conditions determine climate that affects life on Earth. Whereas fresh water in lakes and rivers covers less 1%, its contamination significantly damages ecosystems. Within this research this paper proposes a framework with a custom protocol stack for river monitoring with hybrid network topology. The main goal is to design and implement a framework of distributed network of navigating autonomous underwater vehicles (AUV) and fixed sensors for rivers that will collect monitoring information and transmit data to the central base station. Proposed framework perfectly fits into the latest notion of internet of underwater things architecture and in future it can be utilised not only for shallow river monitoring but also in such extended applications as pipeline surveillance, harbour security and fish farms monitoring.