In an era when flood phenomena intensify worldwide, the scarcity of proper and systematic flood flow measurements has become a conundrum. As an answer, the non-intrusive Large-Scale Particle Image Velocimetry (LSPIV) method has recently advanced to a contemporary gauging alternative, though several limitations in the field application pose questions. To tackle relevant restrains, this study brings forth a new approach for LSPIV field applications and flood gauging using lightweight unmanned aerial vehicles (UAV). In the core of the suggested approach lies a flexible yet direct and accurate matching technique to define the water surface as reference plane, without the need for fixed Ground Control Points (GCP) on the field. In addition, to address uncertainties relevant to apparatus movements that occur from winds and gusts during field recordings, an error-removing process that utilises digital fictitious GCPs is reported. The proposed techniques, implemented via a purpose-built application, are evaluated under various recording conditions in both laboratory and field studies, with positive results. Overall, the granted autonomy, as a result of the approach, provides applicability of the LSPIV method to practically any section of interest without the need for construction or the presence of personnel in hazardous conditions, allowing for a safe, efficient, and low-cost flood gauging alternative.