Coastal estuaries are among the most dynamic and ecologically sensitive environments, yet they are increasingly threatened by anthropogenic activities and climate-related stressors. This study investigates three decades (1990–2020) of shoreline dynamics in three major estuaries along the northern Persian Gulf—Bidkhoon, Ziarat, and Shif—each exhibiting distinct morphodynamic characteristics and varying degrees of human influence. Using multi-temporal Landsat imagery within a GIS environment, shoreline positions were extracted using the Modified Normalized Difference Water Index (MNDWI) and analyzed with the Digital Shoreline Analysis System (DSAS). Shoreline change was quantified using the Net Shoreline Movement (NSM) and Linear Regression Rate (LRR) metrics. Mean LRR values of −1.4, −9.02, and −25.2 m yr⁻¹ were estimated for the Bidkhoon, Ziarat, and Shif estuaries, respectively. Bidkhoon, which lacks significant fluvial sediment input, exhibited a predominantly erosional shoreline with relatively low spatial variability, suggesting a largely tide-dominated coastal system. Shif experienced the largest absolute shoreline fluctuations (maximum NSM erosion: −2332.17 m; maximum accretion: +1326.85 m) and displayed a complex pattern of alternating erosion and accretion, with localized retreat within the Helleh River delta and shoreline progradation elsewhere, likely associated with aquaculture development and sediment redistribution. Ziarat exhibited the most pronounced shoreline retreat, reaching a maximum NSM of −989.86 m, consistent with reduced sediment supply following the construction of the Salman Dam. Regional relative sea-level rise and land subsidence may have further contributed to shoreline retreat, particularly within the Mond River delta. Although all three estuaries are located within protected coastal areas characterized by limited urban and industrial development, the observed shoreline changes demonstrate that both natural coastal processes and human ac