The current study focuses on analyzing the impacts of climate change and land use/land cover (LULC) changes on sediment yield in the Puthimari basin, an Eastern Himalayan sub-watershed of the Brahmaputra, using a hybrid SWAT-ANN model approach. The analysis was meticulously segmented into three distinct time spans: 2025–2049, 2050–2074, and 2075–2099. This innovative method integrates insights from multiple climate models under two Representative Concentration Pathways (RCP4.5 and RCP8.5), along with LULC projections generated through the Cellular Automata Markov model. By combining the strengths of the Soil and Water Assessment Tool (SWAT) and artificial neural network (ANN) techniques, the study aims to improve the accuracy of sediment yield simulations in response to changing environmental conditions. The non-linear autoregressive with external input (NARX) method was adopted for the ANN component of the hybrid model. The adoption of the hybrid SWAT-ANN approach appears to be particularly effective in improving the accuracy of sediment yield simulation compared to using the SWAT model alone, as evidenced by the higher coefficient of determination value of 0.74 for the hybrid model compared to 0.35 for the standalone SWAT model. In the context of the RCP4.5 scenario, during 2075-99, the study noted a 29.34% increase in sediment yield, accompanied by simultaneous rises of 42.74% in discharge and 27.43% in rainfall during the Indian monsoon season, spanning from June to September. In contrast, under the RCP8.5 scenario, for the same period, the increases in sediment yield, discharge, and rainfall for the monsoon season were determined to be 116.56%, 103.28%, and 64.72%, respectively. The present study's comprehensive analysis of the factors influencing sediment supply in the Puthimari River basin fills an important knowledge gap and provides valuable insights for designing proactive flood and erosion management strategies. The findings from this research are crucial for understanding the vulnerability of the Puthimari basin to climate and land use changes, and by incorporating these findings into policy and decision-making processes, stakeholders can work towards enhancing resilience and sustainability in the face of future hydrological and environmental challenges.