Floods are phenomenon with significant socio-economic implications mainly for human loss, agriculture, livestock, soil loss and land degradation, for which many researchers try to identify the most appropriate methodologies by analyzing their temporal and spatial development. This study therefore attempts to employ the GIS-based multi-criteria decision analysis and analytical hierarchy process techniques to derive the flood risks management on rice productivity in the Gishari Agricultural Marshland in Rwamagana district, Rwanda. Here, six influencing potential factors to flooding, including river slope, soil texture, Land Use Land Cover through Land Sat 8, rainfall, river distance and Digital Elevation Model are considered for the delineation of flood risk zones. Data acquisition like Landsat 8 images, DEM, land use land cover, slope, and soil class in the study area were considered. Results showed that if the DEM is outdated or inaccurate due to changes in the terrain, such as construction, excavation, or erosion, the predicted flood patterns might not reflect the actual water flow. This could result unexpected flood extents and depths, potentially inundating rice fields that were not previously at risk and this, expectedly explained that the increase 1 m in elevation would reduce the rice productivity by 0.17% due to unplanned flood risks in marshland.