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Floods can cause extensive damage proportional to their magnitude, depending on the watershed hydrology and terrain characteristics. Flood studies generally assume bathymetry as steady, while in reality it is constantly changing due to sediment transport. This study seeks to quantify the impact of different lake bathymetry conditions on flood dynamics. The Hydrotel and Telemac2D models are used to simulate floods for a lake with bathymetries from multiple year surveys. The bathymetries differ in bed elevation due to sediment accumulation and/or remobilisation. Results show that bathymetric differences produce a more noticeable effect for moderate flows than for maximum flows. During moderate flows, shallower bathymetries induce higher water levels and larger water extents. For peak flows, differences in water levels and extent are practically negligible for the different bathymetries tested. Higher water levels during moderate flows could produce longer flooding times and affect the community’s perception of flood impacts.