The spatial heterogeneity of microtopography where variation in elevation is less than a meter plays a significant role in ecological, hydrological, and biogeochemical processes. The microtopography can be categorized into microtopographic features as in the case of forested wetlands in hummocks (local high points), and hollows (local low points).To quantify and assess these microtopographic features, close-range remote sensing technologies can be used in combination with field surveys. This research provides a systematic framework for microtopographic studies using these technologies such as sUAS, aerial LiDAR, and terrestrial LiDAR. We highlight the importance of using high-resolution DEM of less than 1m2 spatial resolution to delineate microtopography. In a low-relief topography, especially in coastal forested wetlands wherehollows and hummocks are differentiated by a few centimeters, we demonstrated a method by combining water level data and terrestrial LiDAR-based DEM to characterize microtopography over a large aerial extent utilizing coarser resolution aerial LiDAR data. This research also investigated the influence of microtopography on carbon dynamics in tidal and non-tidal coastal forested wetlands and found overestimation of ground elevation can not only misclassify the microtopographic features but also leads to an underestimation of CH4 flux (upto 74%) and overestimation of the CO2 flux (upto 44%). Our results show that the combination of on-site water level data and RTK GPS ground-truthed terrestrial LiDAR-based elevation data can be used to successfully adjust the base elevation and classification of microtopographic features in aerial LiDAR data. The substitution of the more variable and drier nontidal water table regime in the process-based model resulted in a significant impact on C gas emissions with annual CH4 emissions decreasing by an average of approximately 53% and CO2 emissions increasing twofold over the four-year study period. The C gas flux extrapolation based on these LiDAR-based DEM over larger areas possibly at the watershed scale may open new avenues for research and can provide insight as to how wetland microtopography interacts with precipitation/ET and tidally influenced hydrologic regimes and how these may change under rising sea levels to impact GHG emissions and carbon cycling in bottomland hardwood forests.