Marine food chains are highly stressed by aggressive fishing practices and environmental damage. Aquaculture has increasingly become a source of seafood which spares the deleterious impact on wild fisheries. However, continually monitoring water quality to successfully grow and harvest fish is labor intensive. The Hybrid Aerial Underwater Robotic System (HAUCS) is an Internet of Things (IoT) framework for aquaculture farms to relieve the farm operators of one of the most labor-intensive and time-consuming farm operations: water quality monitoring. To this end, HAUCS employs a swarm of unmanned aerial vehicles (UAVs) or drones integrated with underwater measurement devices to collect the in situ water quality data from aquaculture ponds. A critical aspect in HAUCS is to develop an effective path planning algorithm to be able to sample all the ponds on the farm with minimal resources (i.e., the number of UAVs and the power consumption of each UAV). Three methods of path planning for the UAVs are tested, a Graph Attention Model (GAM), the Google Linear Optimization Package (GLOP) and our proposed solution, the HAUCS Path Planning Algorithm (HPP). The designs of these path planning algorithms are discussed, and a simulator is developed to evaluate these methods’ performance. The algorithms are also experimentally validated at Southern Illinois University’s Aquaculture Research Center to demonstrate the feasibility of HAUCS. Based on the simulations and experimental studies, HPP is particularly suited for large farms, while GLOP or GAM is more suited to small or medium-sized farms.