The aim of this study was to investigate the sediment dynamics in the largest lagoon in Europe (Curonian Lagoon, Lithuania) through the analysis of in situ data and the application of a sediment transport model. This approach allowed to identify the propagation pathway of the riverine suspended sediments, to map erosion-accumulation zones in the lagoon and calculate the sediment budget over a 13-year-long simulation. Sampled suspended sediment concentration data are important for understanding the characteristics of the riverine and lagoon sediments, and show that the suspended organic matter plays a crucial role on the sediment dynamics for this coastal system. The numerical experiments carried out to study sediment dynamics gave satisfactory results and the possibility to get a holistic view of the system. The applied sediment transport model with a new formula for settling velocity was used to estimate the patterns of the suspended sediments and the seasonal and spatial sediment distribution in the whole river–lagoon–sea system. The numerical model also allowed understanding the sensitivity of the system to strong wind events and the presence of ice. The results reveal that during extreme storm events, more than 11.4 × 106 kg of sediments are washed out of the system. Scenarios without ice cover indicate that the lagoon would have much higher suspended sediment concentrations in the winter season comparing with the present situation with ice. The results of an analysis of a long-term (13 years) simulation demonstrate that on average, 62% of the riverine sediments are trapped inside the lagoon, with a marked spatially varying distribution of accumulation zones.