Unmanned aerial vehicles (UAVs) have become the state of the art remote sensing measuring methodology in many engineering fields. The systems are becoming increasingly autonomous, and have a growing number of potential applications with decreasing costs. This makes UAV-based data acquisition a efficient and effective tool for surveying hydrosystems such as riverine ecosystems. In this work, we present our use of a lightweight multi-camera system specially designed for UAVs, generating total spatial coverage spectral imagery in reference reaches in Thailand. High resolution maps of the Normalized Differenced Vegetation Index (NDVI) are generated using near infrared (NIR) imagery gathered by the multi camera system. This hybrid approach can provide the necessary input data for detailed studies of the interaction between hydromorphological conditions and terrestrial vegetation caused by a living weir structure. In addition, digital surface models (DSM) are produced with the structure from motion (SfM) method, were the most effective models are made from a combination of imagery from high resolution aerial photography, supported by the inclusion of terrestrial photography. In this work, we show how the UAV-base aerial imagery and image processing workflow can be leveraged to enable the creation of a detailed quantitative metrics which can then be used in the analysis of ecologically complex monitoring sites.