Mangrove wetlands are natural barriers which purify inland pollution and reduce its flux to the ocean, which plays an important role in controlling coastal water nutrient and nutrients cycling. Sediment, water, and vegetation cooperate with each other to maintain the normal function of mangrove wetland ecosystems. Among them, sediment is an important place for benthic organism activity, landsea interface material exchange, pollutant containment, and self-purification. Pore-water acts as a crucial medium for material exchange in the water-sediment interface, as it is closely related to the migration, release and transformation of pollutants. Understanding the characteristics of sediment and pore-water in mangrove ecosystems has some guiding significance for mangrove wetland health evaluation. In this study, the characteristics of sediment and pore-water in mangrove ecosystems with and without shrimp aquaculture effluent discharge in the area were analyzed. The results were as follows: (1) Total nitrogen, total phosphorus, and organic matter have positive synergistic effects in the shrimp aquaculture effluent discharge area, and the effluent has an obvious acidification effect on sediment; (2) NH₄⁺ is main component of dissolved inorganic nitrogen (DIN) in mangrove sediment, and the accumulation of NO₃^-, NO₂^- and DIN in sediment increased with the discharge of shrimp aquaculture effluent. The change of physiochemical properties of sediment and pore-water is a synergistic process, which can be a quantitative indicator to evaluate habitat evolution of mangrove in shrimp aquaculture areas.