The integration of mangrove management with aquaculture, termed the silvofishery pond system, has been implemented in Berau Regency, East Kalimantan Province, Indonesia. A detailed survey was conducted to assess the features of mangrove terrain surrounding silvofishery ponds, aiming to enhance the productive and sustainable management of these mangrove areas in Berau Regency. This survey focused on various land characteristics such as topography, tidal patterns, water quality, soil properties, climate, and the state of mangrove vegetation. The health of mangrove vegetation was assessed by calculating the Important Value Index (IVI) across different growth stages: trees, saplings, and seedlings. The findings reveal that the mangrove adjacent to the silvofishery ponds in Berau Regency are home to 14 species from 13 genera and 10 families. Rhizophora mucronata displayed the highest IVI scores across all growth stages: 75.17% for trees, 93.14% for saplings, and 66.98% for seedlings, the latter shared with Rhizophora apiculata. Soil quality emerged as a critical limiting factor for land use in silvofishery ponds, particularly due to high potential acidity (low pH) and low nitrogen (N) content. To enhance soil quality, it is recommended that soil management practices such as remediation (via drying, submerging, flushing, or liming) and N supplementation through fertilization be employed. Furthermore, given the sparse mangrove vegetation density at the tree level (1,012 trees/ha), efforts to promote natural mangrove regeneration and prevent deforestation and degradation are advised. Considering the unique characteristics of the mangroves, the implementation of the komplangan model—a silvofishery approach that segregates mangroves restoration pond from grow-out ponds—is recommended to boost productivity and ensure sustainability in the coastal region of Berau.