Plastic pollution has a severe impact on the ecosystem, altering its natural equilibrium and causing serious health issues to both flora and fauna. Several actions have already been undertaken in order to reduce the plastic litter dispersion in the environment, both in terms of changing the human behavior, reducing the use of plastics and avoiding their dispersion, and of implementing methods for detecting and collecting the already dispersed ones. This paper focuses on the latter, and, in particular, on plastic litter detection on the fluvial environment. To this aim, an Unmanned Aerial Vehicle, provided with a multi-spectral and a thermal camera, have been used, in order to: (i) allow affordable periodic monitoring of relatively long river reaches, (ii) detect even quite small macro-plastics, based on their spectral signature. More specifically, since the cameras deployed in our data collection campaigns are not synchronized, this work aims at presenting the developed strategy for the co-registration of the acquired imagery, which results to be quite challenging given the few amount of visual features recognizable on the images acquired flying at a limited altitude over a river. The proposed methodology, which is based on the correlation maximization between multi-spectral and thermal images, provided reasonable results on the considered case study. The obtained values of normalized intersection over union of plastic areas are over 80%.