Climate change is a major challenge in arid and semi-arid regions, significantly affecting water resources by disrupting the hydrological cycle. The present study aims to analyze historical trends in temperature and precipitation, assess changes in annual Water Yield, and examine future climate projections in the Maharloo Wetland Basin, located in Fars Province, Iran. To achieve this, reanalysis datasets from ERA5-Land and TerraClimate were used for the historical period (1991–2022), and downscaled outputs of selected CMIP6 models were applied for the near-future period (2021–2040) under two emission scenarios: SSP2-4.5 and SSP5-8.5. The Mann–Kendall and Sen’s slope tests revealed significant increasing trends (1 to 3°C) in all temperature indices (both extremes and means) over the past three decades. Notably, nighttime and winter warming has dominated, resulting in a reduced diurnal and seasonal temperature range. Annual precipitation also showed a declining trend, with the sharpest reduction observed in the western sub-basin of the lake, which is the main source of inflow to the Maharloo Wetland. In this area, the reduction in Annual Water Yield exceeded the decline in precipitation, which may be attributed to changes in rainfall intensity and temporal distribution, as well as increased evapotranspiration in warmer years. Satellite imagery confirmed the decreasing water body area of the wetland. Future climate projections suggest continued warming between 1.1°C and 1.5°C and a slight increase in precipitation (3–6%), though future warming is expected to be more intense during daytime and summer months. If current trends persist, the region may face further wetland desiccation, increased saline dust storms, and accelerated desertification—underscoring the urgent need for climate adaptation strategies.