Rain gardens are green stormwater infrastructure that are designed to leverage natural processes to mitigate the impacts of urban stormwater through capturing, infiltrating, and filtering run off. Overtime these systems have the potential to buildup fines and nutrients, impacting their sustainable function. A rain garden’s performance depends on its ability to infiltrate runoff which can be reduced by clogging. Another concern is the potential transport of contaminants from rain gardens to groundwater through deep drainage. This study analyses the spatial and temporal distribution of fines and nutrients in three rain gardens through comprehensive field tests, laboratory testing, and computation analysis. Geomorphic studies were performed by integrating the digital elevation models, derived from Lidar surveys, with the FastMech solver within International River Interface Cooperative (iRIC) software, to model shear stress distribution and sediment transport relative to spatial observations of soil texture and nutrient concentrations within the rain garden. The soil properties were also used in creating models of water infiltration and nutrient sorption using Hydrus 1D. Results show that shear stresses in localized sections of each rain garden can be correlated with fines and nutrient distributions, allowing for prioritizing locations for maintenance. To conclude, LiDAR scans, flow and shear stress models, infiltration and nutrient transport models, field and laboratory soil tests can help us understand the surface dynamics and soil attributes, and gradually gain insight into the GSI performance with time.