Present study is dedicated to assessment and mapping of generation and propagation potential of flash flood and river floods on the rivers of the Republic of Moldova. Main methods applied in the research are Flash Flood Potential Index (FFPI) and Flooding Potential Index (FPI). Additionally, a new index for estimation of flood propagation potential (FPPI) is proposed in order to evaluate impact of main factors (natural and human) on propagation of flood wave through the floodplain of small and medium-sized rivers of Moldova. In total, assessment of FFPI an FPI was performed for 789 elementary river basins (basin area less than 200 km2) and also was considered for 983 elementary territorial-administrative units (communes). Estimation of FPPI was made for 50 main small and medium sized rivers of Moldova. All index parameters (7 for FFPI, 6 for FPI and 12 for FPPI) were integrated, analyzed and combined in GIS environment. As a results, it was found that the FFPI is average for mostly all basins and communes but is characterized by significant differences in spatial representation on local level. FPI is high in basins and communes situated in the floodplains of large and medium sized rivers, in flood-prone areas, and is low in those with high altitudes and steep slopes (Codri and Nistru heights). Flood propagation potential was estimated with average values for 56% of total number of rivers, high for 34% and very high for 6%. The results can be used for future estimation of flood generation and flood wave propagation processes and for improvement and optimization of flood management practices and strategies on rivers weakly studied from hydrology point of view.