AbstractThere is growing interest in the use of Unoccupied Aerial Systems (UAS) for mapping and monitoring of seagrass habitats. UAS provide flexibility with timing of imagery capture, are relatively inexpensive, and obtain very high spatial resolution imagery compared to imagery acquired from sensors mounted on satellite or piloted aircraft. However, research to date has focused on UAS applications for exposed intertidal areas or clear tropical waters. In contrast, submerged seagrass meadows in temperate regions are subject to high cloud cover and water column turbidity, which may limit the application of UAS imagery for coastal habitat mapping. To test the constraints on UAS seagrass mapping, we examined the effects of five environmental conditions at the time of UAS image acquisition (sun angle, tidal height, cloud cover, Secchi depth and wind speed) and five site characteristics (eelgrass patchiness and density, presence and density of non‐eelgrass submerged aquatic vegetation, sediment tone, eelgrass deep edge and site exposure) at 26 eelgrass (Zostera marina) monitoring sites in British Columbia, Canada. Eelgrass was delineated in UAS orthomosaics using object‐based image analysis, combining image segmentation with manual classification. Each site was ranked according to the analysts’ confidence in the delineated eelgrass. Robust Linear Regression revealed sun angle and ‘theoretical visibility’ (an aggregate of tidal height, Secchi depth, and eelgrass deep edge conditions) to be the most important variables affecting mapping confidence. In general, ideal environmental conditions to obtain high confidence eelgrass mapping included: (1) sun angles below 40°; (2) positive theoretical visibility with Secchi depths >5 m; (3) cloud cover conditions of <10% or >90%; and (4) wind speeds less than 5 km h−1. Additionally, high mapping confidence was achieved for sites with dense, continuous, and homogeneous eelgrass meadows. The results of this analysis will guide implementation of UAS mapping technologies in coastal temperate regions.