The Pemali River estuary in Brebes is a mangrove rehabilitation area. Mangrove cover has increased significantly over the past two decades. However, it still faces anthropogenic pressures that may affect carbon storage and physiological responses. This study aimed to evaluated mangrove carbon stock distribution by stand age and examined its relationship with proline accumulation, a biomarker of abiotic stres. Field data were collected from July to September 2025 at three stations representing different mangrove stand ages (>15 years, 10–15 years, and <5 years). Vegetation structure was assessed based on species composition and stem diameter, while biomass was estimated using specific allometric equations. Sediment analysis included organic carbon, nitrate, and phosphate, while leaf proline levels were analyzed using a colorimetric method. The relationship between carbon stocks, proline levels, and environmental parameters was evaluated using multivariate analysis (PCA). The results showed that Rhizophora mucronata dominated all stations. Older mangrove stands (>15 years) had the highest biomass and carbon stocks, estimated at 805.42–945.28 mg/kg. Sediment organic C was also highest in older mangroves (0.93–2.24%) and decreased in younger areas. Proline concentrations ranged from 0.018–0.434 mg/g, peaking in Acanthus ilicifolius at low pH and dry conditions. PCA showed sediment organic C correlated with salinity, DO, temperature, and sediment nutrients. Proline was negatively correlated with pH, TDS, and salinity, and positively with water phosphate.