The occurrence of localised nutrient loading in small coastal communities of the Mediterranean threatens the functionality of seagrass ecosystems, underscoring the need to reliably identify their onset and magnitude. However, short-term measurements of nutrient levels can be an inaccurate measure of sustained nutrient loading due to the spatiotemporal variability of coastal hydrodynamics. Alternatively, we examined the suitability of epiphyte assemblages on Posidonia oceanica leaves as indicators of anthropogenic nutrient enrichment of coastal waters for the first time in the eastern Aegean Sea. We studied seagrass biometric and meadow parameters at control and impacted sites, in addition to epiphyte community composition and structure at a depth of 5 m during winter 2022. Sites were classified a priori using a modified version of the Land Use Simplified Index (LUSI). Impacted meadows exhibited lower leaf length and shoot density, as well as higher epiphyte cover and biomass. The composition of epiphyte communities shifted significantly, with clear differences observed in red coralline algae, filamentous brown algae, and annelids. Our results indicated that potentially increased nutrient availability from point and diffuse sources, such as wastewater discharge and agricultural activity, may have affected seagrass bed condition. We observed substantial epiphyte cover, causing both direct (shading) and indirect (intensified grazing pressure; physical instability of leaves) effects. Our study demonstrates that epiphyte communities, in combination with the LUSI, serve as accurate and cost-effective indicators of nutrient loading in coastal waters. Regular monitoring could enable early detection of elevated nutrient levels and help prevent the long-term decline of seagrass meadows.