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, have growing potential applications, and prices are decreasing. This makes UAV-based data acquisition a very efficient and cost-effective tool for surveying hydrosystems and 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 allows for detailed study of the interactions between hydromorphological conditions and terrestrial vegetation on a living weir structure. In addition, digital surface models (DSM) are produced with structure from motion (SfM) method, were the most effective models are made from a combination of imagery from high resolution aerial photography as well as terrestrial photography.  In this work we show how the UAV-base aerial imagery and image processing workflow can be leveraged to assess highly dynamic hydraulic and morphological conditions, both in space and in time. The proposed methods enable the creation of a detailed quantitative analysis of ecologically complex monitoring sites.