This paper presents a comparative analysis of cluster‐based selection protocols for wireless sensor networks (WSNs) in smart irrigation systems. The study evaluates the performance of stable election protocol (SEP)‐based protocols, including conventional SEP, zonal SEP (ZSEP), enhanced SEP (ESEP) and threshold‐sensitive SEP (TSEP), and distributed energy‐efficient clustering (DEEC)‐based protocols, including conventional DEEC, developed DEEC (DDEEC), enhanced DEEC (EDEEC) and threshold‐sensitive DEEC (TDEEC). Simulation results show that TSEP and ZSEP outperform other SEP‐based protocols in terms of network lifetime, stability period, number of dead nodes and throughput. EDEEC and TDEEC show superior performance compared to other DEEC‐based protocols. However, TDEEC and EDEEC have a lower performance in terms of packets sent to cluster heads (CHs) due to the three levels of energy heterogeneity, which reduce the average packets sent to CHs. Finally, a comparative analysis between the SEP‐based and DEEC‐based protocols is presented. The findings reveal that TSEP outperforms all other protocols in terms of the performance metrics examined in this paper, except for throughput, which is higher in the case of ZSEP. Overall, the proposed cluster‐based selection protocols improve the energy efficiency and lifetime of WSNs in smart irrigation systems, and the results demonstrate their effectiveness in supporting the performance of smart irrigation systems.