We propose a novel method for constructing a pseudo‐synoptic view of estuarine features from non‐synoptic observations captured by mobile platforms. The model‐aided Lagrangian interpretation (MALI) method is based on relocating observations to a common reference moment in time along three‐dimensional Lagrangian trajectories derived from a numerical model of estuarine circulation. The method relies on the model skill to capture large‐scale circulation features, and on high‐resolution in situ observations to characterize small‐scale hydrographic structure. We demonstrate our technique by applying MALI to autonomous underwater vehicle observations in the Columbia River estuary, with the aid of a validated unstructured‐grid finite‐element numerical simulation. The method can be readily adapted to a broader range of environments, observational platforms, and model‐data combinations.