Uncrewed-Aerial Vehicles (UAVs) and hyperspectral sensors are emerging as effective alternatives for monitoring water quality on-demand. However, image mosaicking for largely featureless coastal water surfaces or open seas has shown to be challenging. Another pertinent issue observed is the systematic image misalignment between adjacent flight lines due to the time delay between the UAV-borne sensor and the GNSS system. To overcome these challenges, this study introduces a workflow that entails a GPS-based image mosaicking method for push-broom hyperspectral images, together with a correction method to address the aforementioned systematic image misalignment. An open-source toolkit, CoastalWQL, was developed to facilitate the workflow, which includes essential pre-processing procedures for improving the image mosaic’s quality, such as radiometric correction, de-striping, sun glint correction, and object masking classification. For validation, UAV-based push-broom hyperspectral imaging surveys were conducted to monitor coastal turbidity in Singapore, and the implementation of CoastalWQL’s pre-processing workflow was evaluated at each step via turbidity retrieval. Overall, the results confirm that the image mosaicking of the push-broom hyperspectral imagery over featureless water surface using CoastalWQL with time delay correction enabled better localisation of the turbidity plume. Radiometric correction and de-striping were also found to be the most important pre-processing procedures, which improved turbidity prediction by 46.5%.