Water quality monitoring systems that are enabled by the Internet of Things (IoT) and used in water applications to collect and transmit water data to data processing centers are often resource-constrained in terms of power, bandwidth, and computation resources. These limitations typically impact their performance in practice and often result in forwarding their data to remote stations where the collected water data are processed to predict the status of water quality, because of their limited computation resources. This often negates the goal of effectively monitoring the changes in water quality in a real-time manner. Consequently, this study proposes a new resource allocation method to optimize the available power and time resources as well as dynamically allocate hybrid access points (HAPs) to water quality sensors to improve the energy efficiency and data throughput of the system. The proposed system is also integrated with edge computing to enable data processing at the water site to guarantee real-time monitoring of any changes in water quality and ensure timely access to clean water by the public. The proposed method is compared with a related method to validate the system performance. The proposed system outperforms the existing system and performs well in different simulation experiments. The proposed method improved the baseline method by approximately 12.65% and 16.49% for two different configurations, demonstrating its effectiveness in improving the energy efficiency of a water quality monitoring system.