The development of China’s digital waterways has led to the extensive deployment of cameras along inland waterways. However, the limited processing and utilization of digital resources hinder the ability to provide waterway services. To address this issue, this paper introduces a novel waterway perception approach based on an intelligent navigation marker system. By integrating multiple sensors into navigation markers, the fusion of camera video data and automatic identification system (AIS) data is achieved. The proposed method of an enhanced one-stage object detection algorithm improves detection accuracy for small vessels in complex inland waterway environments, while an object-tracking algorithm ensures the stable monitoring of vessel trajectories. To mitigate AIS data latency, a trajectory prediction algorithm is employed through region-based matching methods for the precise alignment of AIS data with pixel coordinates detected in video feeds. Furthermore, an augmented reality (AR)-based traffic situational awareness framework is developed to dynamically visualize key information. Experimental results demonstrate that the proposed model significantly outperforms mainstream algorithms. It achieves exceptional robustness in detecting small targets and managing complex backgrounds, with data fusion accuracy ranging from 84.29% to 94.32% across multiple tests, thereby substantially enhancing the spatiotemporal alignment between AIS and video data.