This research uses a process-based model (Delft3D), validated with measured wave data, to investigate the controls that a cuspate shoreline and its associated submerged morphology have on wave generation, propagation and attenuation within a large elongated lagoon (Lagoa dos Patos, Brazil). A method based on the Energy-Flux-Method was applied to the historical wind dataset to define representative wind cases to be used as forcing conditions in the model. The results show that, during extreme wind conditions, the spits dissipate wave energy in the lagoon. This (wave attenuation and the wave sheltering effect) controls the stability of the adjacent coastline. The wave attenuation varies between 18 and 46% along the submerged spit depending on the crest width and the amplitude of the incident waves. Waves are mainly attenuated in the proximal and central portions of the spits where the spits are wider, resulting in a reduced transmitted energy to the adjacent coastline, while larger waves are also attenuated on the distal end of the spits. The degree of attenuation depends on the direction of wave generation, the respective fetch, the spit width, and the water depth. A strong relationship of mutual co-adjustment between the morphology and the wave field results in a very low occurance of oblique wave angles of incidence, especially for waves propagating accross the long lagoon axis. Furthermore, the wave attenuation over the spits is also responsible for its progressive erosion, which from decades to centuries, may lead to an increase of changes on the lagoon shorelines.