Unmanned aerial systems (UAS) are widely used in the acquisition of high-resolution information in the marine environment. Although the potential applications of UAS in marine habitat mapping are constantly increasing, many limitations need to be overcome—most of which are related to the prevalent environmental conditions—to reach efficient UAS surveys. The knowledge of the UAS limitations in marine data acquisition and the examination of the optimal flight conditions led to the development of the UASea toolbox. This study presents the UASea, a data acquisition toolbox that is developed for efficient UAS surveys in the marine environment. The UASea uses weather forecast data (i.e., wind speed, cloud cover, precipitation probability, etc.) and adaptive thresholds in a ruleset that calculates the optimal flight times in a day for the acquisition of reliable marine imagery using UAS in a given day. The toolbox provides hourly positive and negative suggestions, based on optimal or non-optimal survey conditions in a day, calculated according to the ruleset calculations. We acquired UAS images in optimal and non-optimal conditions and estimated their quality using an image quality equation. The image quality estimates are based on the criteria of sunglint presence, sea surface texture, water turbidity, and image naturalness. The overall image quality estimates were highly correlated with the suggestions of the toolbox, with a correlation coefficient of −0.84. The validation showed that 40% of the toolbox suggestions were a positive match to the images with higher quality. Therefore, we propose the optimal flight times to acquire reliable and accurate UAS imagery in the coastal environment through the UASea. The UASea contributes to proper flight planning and efficient UAS surveys by providing valuable information for mapping, monitoring, and management of the marine environment, which can be used globally in research and marine applications.