Embayed sandy beaches are dynamically complex systems that vary in time and space. The rising demand for the uses and resources associated with these environments may neglect the shoreline mobile nature and lead to imbalances in the beach sediment budget. Climate change imminence has been increasing coastal risks, with a considerable contribution of local and regional causes. This study aims to assess the influence of short to long-term processes on short spatial scales and to identify which processes control the behavior of neighboring beaches. Thereby, a case study was analyzed at Barra Beach (BB) and Ferrugem Beach (FB), a small embayment separated by an intermittent inlet located in Garopaba, Santa Catarina state, southern Brazil. The shoreline dynamic behavior of both beaches was assessed through a multi-temporal approach (historical and geological), investigating the main factors influencing their morphodynamic behavior. The historical variation was investigated through shoreline change rates along 16 years (2003–2019), calculated with Digital Shoreline Analysis System (DSAS) v5.0 – ESRI® ArcGis extension, considering past shoreline positions extracted from satellite imagery. Geological evolution was analyzed in terms of seismostratigraphy through subsurface profiles acquired with a Ground Penetrating Radar (GPR) system. Interdecadal shoreline change rates and GPR records indicated that BB has a transgressive shoreline in a retrogradational barrier, while FB is slightly progradational, with a stable shoreline from the historical scale perspective. The interannual analysis showed that the inlet surroundings are influenced by seasonality, and beach rotation was not detected between the beaches nor within themselves. The distinct morphodynamic behavior between BB and FB is a function of their shoreline geometry, architectural elements, wave energy distribution, and sediment sources/sinks, resulting in variant alongshore sediment budgets. Overall, this paper highlights the importance of local shoreline assessment, and it could enhance efficient present-day coastal management, supporting future sustainable urban planning.