Real-time and high-precision situational awareness technology is critical for autonomous navigation of unmanned surface vehicles (USVs). In particular, robust and fast obstacle semantic segmentation methods are essential. However, distinguishing between the sea and the sky is challenging due to the differences between port and maritime environments. In this study, we built a dataset that captured perspectives from USVs and unmanned aerial vehicles in a maritime port environment and analysed the data features. Statistical analysis revealed a high correlation between the distribution of the sea and sky and row positional information. Based on this finding, a three-branch semantic segmentation network with a row position encoding module (RPEM) was proposed to improve the prediction accuracy between the sea and the sky. The proposed RPEM highlights the effect of row coordinates on feature extraction. Compared to the baseline, the three-branch network with RPEM significantly improved the ability to distinguish between the sea and the sky without significantly reducing the computational speed. •A new network with RPEM was proposed to improve the prediction accuracy of sea, sky, and small obstacles.•A novel RPEM was proposed to emphasise the influence of row coordinates on feature extraction.•A dataset was built in the maritime port environment, which contains the data from the view of both the USVs and UAVs.