Recent work on Integrated Assessment Models (IAMs) has tried to assess and include impacts of climate change with macroeconomic representations. Although several studies focus on geophysical climate impacts on the water, energy, and land (WEL) sectors (e.g., precipitation, crop yields, cooling degree days), most IAMs still do not include these impacts and therefore underestimate the consequences on multiple sectors. Using the latest version of the MESSAGEix-GLOBIOM IAM with an explicit representation of the WEL systems, we include climate impacts on the natural system (e.g., water cycle and crop yields changes) and on technologies (e.g., power plant potentials, desalination, etc.) for different sectors. This framework allows comparing mitigation and adaptation scenarios with the corresponding climate impacts in the WEL sectors which affect decision-making on crop choices, water use, and energy production and demands in a system-explicit way that was neglected in previous scenarios. In addition, using uncertainty ranges directly from climate and hydrological models avoids additional error-propagative steps. We develop and compare updated global mitigation scenarios to achieve the 1.5C by 2100 to adaptation scenarios with climate corresponding to Representative Concentration Pathway (RCP) 2.6 and RCP 6.0 respectively. Here we show that adding geophysical sector-explicit climate impacts not only affects the investment balance between scenarios but, most importantly, provides new insights into sectoral transitions and regional distribution of mitigation and adaptation costs.