Life Cycle Assessment (LCA) was applied to assess the environmental performance of brackish water polyculture of black tiger prawn, mud crabs, tilapia and milkfish in a pond aquaculture system. The study was conducted on 15 production sites, located in Pampanga Province of the Philippines. The scope of analysis covered the hatchery or capture of juveniles from the wild up to the delivery of products to auction markets. Impact categories included eutrophication, acidification, climate change, land occupation, net primary production use, total cumulative energy demand (TCED), and total human labour. Life cycle impact indicators were calculated for one tonne of product (total production or that of individual species) using both energy-based and economic allocations. The results indicated that the main impacts from farming operations were eutrophication, land occupation, acidification and human labour. Feed (molluscs harvested from aquatic ecosystems) mainly influenced net primary production use, TCED and climate change, and harvesting and delivery mainly influenced climate change and TCED. Differences in farm practices and yields induced high variability in impacts. Production site size had no significant effect; however, its distance from the sea appeared to affect its efficiency and, consequently, impacts. Changing the allocation method changed the ranking of species' impacts within each impact category, milkfish having the highest impacts with energy-based allocation and prawn and crabs having the highest impacts with economic allocation. The lack of differences in impacts between intensive monocultures of prawn and tilapia recorded in the literature and the same species in Pampanga's polyculture suggests that the degree of intensification is not a relevant concept for distinguishing impacts of aquaculture systems.