Coastal archives of changing hydrometeorological conditions include mineralogical anomalies, such as heavy-mineral concentrations (HMCs) of variable thickness and intensity, which contain varying ferrimagnetic (e.g., magnetite) fractions. As an effective alternative to laborious mineralogical and granulometric analysis, we present the first set of bulk-volume low-field magnetic susceptibility (MS) databases from beach and dune lithosomes in the Western Estonian archipelago: Harilaid cuspate foreland (westernmost Saaremaa Island) and Tahkuna strandplain (northernmost Hiiumaa Island). Readings were conducted both in situ from trench walls and on core subsamples. At the Tahkuna site, late Holocene beach ridges reveal substantially lower values: quartz-dominated dune sequences grade from 5–20 μSI downward to diamagnetically dominated (−1–7 μSI) beach facies. Values are higher (20–140 μSI) in historically reactivated parabolic dunes that are encroaching southward over the strandplain. At the Harilaid site, four beach dune ridges (height: 2–3 m) that span the past 250–300 years show a general increase in mean MS from 320–850 μSI with decreasing age, with peaks of 1000–2000 μSI below the dune crests (depth: ~0.3–0.6 m) likely related to contemporary wind acceleration during ridge aggradation. The highest mineralogical anomalies range from 2000–5500 μSI in the historic dune sections and exceed 8000 μSI along the actively eroding upper-berm segments, typical of HMCs generated by moderate storms. MS anomalies are likely correlated with high-amplitude electromagnetic signal responses in georadar records and provide useful information for optical luminescence sampling strategies. Our study demonstrates that magnetic susceptibility trends provide a useful means of rapidly assessing relative temporal changes in overall wave/wind climates, help identify and correlate discrete anomalies related to extreme events, serve as local beach/dune boundary indicators, and represent potentially quantifiable paleo-energy indices.