Weed’s geographical and temporal expansion severely affects the global biodiversity, agricultural ecosystems and economy of the country like India. Therefore, in order to help and better prioritize the management tactics, MaxEnt model was used to predict the current and future distribution of Echinochloa colona and Cyperus rotundus, two economically important weeds of agricultural ecosystems. With the help of 552 and 343 occurrence points of E. colona and C. rotundus, respectively, along with 8 bioclimatic parameters, elevation, and soil layers; modelling was performed and predictions were made for probable hotspots of the species in future changing climate scenario. The area under the receiver operating characteristics (ROC) curve (AUC) was used to test the model’s accuracy, and Jackknife test was used to observe the variable importance for both the species. The model predicts that under Representative Concentration Pathway (RCP) 4.5 for both 2050 and 2070, climatic conditions were generally highly suitable for E. colona, except for certain areas in southern, western, and northern India. Whereas, under RCP 8.5 for the same years, a notable reduction in suitable areas is predicted for the species, particularly in Central India. On the other hand, C. rotundus is projected to contract the suitable areas in future climates under both the scenarios depicting the reduced suitability under future climate. Findings of this study would contribute to a better understanding of the nature of the niche shift of both the species and the potential for invasion under future climate scenarios. This will help in understanding the impact of the species and in making informed decisions on matters related to biodiversity, public health, agriculture, and the economy.