The rice (Oryza sativa L.)–wheat (Triticum aestivum L.) cropping system (RWCS), recognized as the world’s prime agricultural system, plays a pivotal role in global food security by providing employment for millions and ensuring a steady income, thereby serving as a cornerstone for farmers’ livelihoods and attracting numerous investors. However, the sustainability and efficiency of this critical system face momentous threats due to climate change, which affects both the quantity and quality of wheat and rice crops. Currently, the growth frequency of the RWCS has declined, principally due to evolving challenges such as weed infestation, delayed wheat sowing after rice harvest, soil salinity, and the prevalence of various diseases. Among these challenges, weeds pose a considerable threat to the cultivation of both rice and wheat. Seed germination, a crucial stage in the plant life cycle, is influenced by various factors, including dormancy, temperature, moisture, oxygen, and light. A comprehensive understanding of weed ecology is essential for identifying vulnerabilities that can be targeted for improved weed management. Population-based threshold models, including hydro-time and thermal time, provide insights into germination patterns, contributing to the overall fitness of weed species. The ability to predict species’ responses to climate change is paramount, and these models are effective in comprehending and controlling weed emergence behavior across diverse environments. Hence, this review paper emphasizes the reevaluation of current weed management practices, focusing on investigating ecologically sustainable approaches for efficient weed control.