Due to the influence of the environment on the water quality wireless sensor network, it is difficult to replace the node energy at any time, so it must make the most of the little energy available. This work provides a technique that combines cluster head selection, cluster structure creation, and data transmission into one optimal scheme. Firstly, we optimize the cluster head election probability threshold formula on the basis of LEACH and introduce overlap ratio in the competitive mechanism, to avoid excessive overlap between cluster heads. Subsequently, to alleviate the “hot spot” problem caused by multihop, the competitive mechanism of I-LEACH is optimized, which is based on the nonuniform competitive mechanism in the EEUC algorithm when electing the cluster head. Meanwhile, in the structural planning between cluster heads, the optimal path is searched based on the parallelism of genetic algorithm (variable path coding strategy); the combination of I-LEACH and EEUC-IGA, named Energy Balance Multihop Clustering Routing Protocol (BEBMCR), can avoid the emergence of “hot paths” and reduce running time. The simulation results show that BEBMCR still has a longer stable period and higher energy utilization rate under large-scale networks, and node energy consumption is more balanced.