Remote sensing is a valuable tool for surveying submerged aquatic vegetation (SAV) distribution patterns at extensive spatial and temporal scales. Only regular mapping over successive time periods (e.g., months, years) allows for a quantitative assessment of SAV loss or recolonization extent. Still, there are only a limited number of studies assessing temporal changes in SAV patterns. ESA Sentinel-2 (S2) has a high revisiting frequency permitting the multi-temporal assessment of SAV dynamics both seasonally and inter-annually. In the current study, a physics-based IDA (Image Data Analysis) model was used for the reconstruction of past SAV percent cover (%cover) patterns in the Baltic Sea coastal waters based on S2 archived images. First, we aimed at capturing and quantifying intra-annual spatiotemporal SAV dynamics happening during a growing season. Modeling results showed that significant changes took place in SAV %cover: the extent of low-cover (0–30% coverage) and intermediate-cover (30–70% coverage) areas decreased, while high-cover (70–100% coverage) areas increased during the growing period. Secondly, we also aimed at detecting SAV %cover spatiotemporal variations inter-annually (over the years 2016–2022). Inter-annual variability in %cover patterns was greater in the beginning of the vegetation period (May). The peak of the growing period (July/August) showed greater stability in the areal extent of the %cover classes.