Main hydrological disasters that occur in the Republic of Moldova are floods. In the last 70 years (1947-2015) floods caused losses of 583 mil. US$. Thereby, a proportion of 55% of the damage was determined by flash floods and 40% - by fluvial floods. Increasing human impact on environment is considered to be the main factor for modifications of flood runoff regimes. Moldova features intense economic activity resulting in the fact that over 60% of the territory is used for agriculture and almost all rivers’ morphology is heavily modified. Therefore, the evaluation of anthropogenic impact on floods generation and propagation processes is of particular interest. Environmental change scenario modelling was performed to analyze the modification of flood wave hydrograph features with the help of the JAMS/J2000 hydrological model. 11 pilot basins have been utilized for this analysis, which represent different parts of the country. Assessment of land cover changes impact over the past 3 decades on flood runoff was performed by consecutive change of land cover layer for 1982 and 2013 for each flood event. The results showed that land cover changes caused a slight decrease of flood runoff in the northern part of the country (-4-10%) due to processes of basins naturalization in areas that were left fallow with undergoing natural succession. In the central and southern rivers basins an increase of flood features could be identified (+2-35%) because of intensified agricultural and urbanization processes. Assessment of reservoir impact on floods was performed on example of the Byc River, which is subject to change due to the Ghidighici reservoir. Thus, first, hydrological model was calibrated and validated for the Byc River natural runoff period and later applied for runoff simulation for the reservoir operation period. Differences of real and naturalized modeled runoff showed that Ghidighici reservoir causes a significant decrease of flood runoff which is from 3 up to 20 times lower than in the case of natural runoff modeling. Resulted hydrological models are well suited for land planning, hydraulic engineering and flood control. They can serve as support for authorities in decision making in flood protection and water resources management.