Pool‐scale growing‐season water‐level reductions (drawdowns) have been implemented on the Upper Mississippi River in an effort to improve fish and wildlife habitat. Aquatic vegetation is a key habitat component, with perennial emergent species, such as Sagittaria latifolia and Sagittaria rigida, especially important. River managers have assumed the need for continuous drawdown during the growing season with limited reflooding and used this guidance in assessing the potential for an ecologically successful drawdown. However, information on the effects of growing‐season flooding episodes on survival and growth of Sagittaria is limited. To assess the flooding tolerance of S. latifoliaand S. rigida, we evaluated multiple levels of timing, duration, and depth on survival and productivity of plants. Plants were produced from S. latifolia and S. rigida seeds and S. latifolia tubers; all were reared under moist‐soil or shallow‐flooded rearing conditions. Mortality of plants was low (2%) among plants from large tubers, low (7%) among seedlings (and largely associated with early flooding treatments), and modest (11%) among plants from small tubers (with no clear effects of inundation). Flooding treatments generally had a positive effect on biomass production from seedlings, particularly when treatments occurred early, were relatively shallow, and were short in duration. There were no clear effects of depth, duration, or timing components of flooding treatments on plant biomass arising from tubers. This experiment indicates that S. latifolia and S. rigida are relatively tolerant of flooding events during the growing season and may actually benefit from some level of inundation.