Very limited information is currently available on growth responses of switchgrass (lowland cultivars) to transient waterlogging in lowland or poorly drained areas. This study investigated impacts of microtopography-induced transient waterlogging on switchgrass (Alamo cultivar) growth, represented by leaf-level gas exchange and biomass yield, in an established experimental field located in the Atlantic coastal plain of North Carolina, USA. Intensive leaf-level gas exchange measurements were conducted on switchgrass at paired spots with distinct elevations in three sub-blocks. Aboveground biomass was randomly collected across the study field to explore the potential impacts of the transient waterlogging on biomass yield. The sum of excess water (SEW) was calculated based on measured instantaneous water table depth to generalize the relationship between biomass yield and intensity of transient waterlogging. Results showed significant (P ≤ 0.0001) treatment effects on leaf-level gas exchange, characterized by evident reduction in both CO2 assimilation rate and stomatal conductance when water table was at or near the soil surface at low positions. Negative impacts of transient waterlogging on leaf-level gas exchange became more evident with the increasing of elevation differences between paired subplots. Stomatal closure was found to be the main mechanism responsible for the decline of net assimilation under transient waterlogging. Aboveground biomass yields of switchgrass showed relatively high spatial variability and were positively and linearly correlated with microtopography (represented by elevation in the analysis) (P < 0.03, R2 > 0.77). Further analysis showed that biomass yields were negatively correlated with SEW (P < 0.001, R2 > 0.6) with an exponential relationship. Results of this study strongly demonstrated transient waterlogging could negatively affect switchgrass growth by suppressing leaf-level gas exchange rates and ultimately reducing biomass yield. Findings from this study have critical implications for evaluating the economic viability of growing switchgrass on marginal lands that are subject to transient waterlogging stresses.