The widespread degradation of mangroves has been attributed to their conversion into other land uses and purposes, most notably their destruction to construct extensive brackishwater aquaculture ponds. This study investigated the relationship between environmental factors and management alternatives for an integrated mangrove-aquaculture system in Derawan Island District, Berau Regency, East Kalimantan Province, Indonesia. The study collected a total of 56 soil and water samples from around 50 ha to assess environmental limiting factors for integrated mangrove-brackishwater aquaculture management. The measured soil quality variables included field pH (pHF), pH of hydrogen peroxide extract (pHFOX), peroxide oxidizable sulfur (SPOS), pyrite (FeS2), organic matter (OM), nitrogen-total (N-TOT), iron (Fe), and aluminum (Al). Water quality variables included salinity, temperature, pH, dissolved oxygen (DO), different forms of nitrogen (NH3–ammonia, NO3–nitrate, and NO2–nitrite), phosphate (PO4), Fe, and total organic matter (TOM). The study employed a hydrological restoration approach to suggest a mangrove-friendly aquaculture pond design and layout. The study generally showed that Acid Sulfate Soils (ASS) significantly restricted the existing mixed-mangrove aquaculture pond management by negatively impacting water quality. This study highlights that, given the characteristics of ASS-affected aquaculture ponds, reducing pond size for shrimp culture (mangrove-to-pond ratio of 80% and 20%) will simplify managing ASS environmental limiting factors through cost-effective remediation techniques and a Balanced Fertilization Strategy (BFS). The reduced shrimp pond size will also provide direct opportunities for mangrove restoration and allow effective hydrological restoration. The economic benefit of the proposed pond design and management model focuses on diversifying production units which include shrimp aquaculture ponds, milkfish or tilapia culture in the peripheral canals of the mangrove compartment, juvenile shrimp production, and periodic harvest from the primary pond canal. The study findings are particularly applicable to ponds that have already been built in ASS to improve productivity in addition to supporting the mangrove rehabilitation program. Converting mangrove and ASS-affected land is not advisable for constructing new aquaculture ponds.