Coastal wetlands have long been identified as ecosystems that can ameliorate N inputs into the ocean. The processes associated with N uptake, transformation, and losses are relatively well understood for temperate wetlands; however, information on tropical wetlands is scarce. In this study, we conducted a whole ecosystem approach to measure N processes within tropical mangroves in the Moresby estuary in northeast Australia. We measured N stocks (trees and soils), inputs from sedimentation, fixation, and accumulation as woody biomass, and outputs through denitrification, anammox, and soil respiration (N₂O emissions). Potential denitrification was detected along anammox (average, min-max) at 883 (485-1,450) gN ha^-1 day^-1, followed by sediment accumulation with 108 (0- 375) gN ha^-1 day^-1, and tree uptake with 93 (13-153) gN ha^-1 day^-1.  Lower rates were found for N fixation with 45 (0-260) gN ha^-1 day^-1 and soil respiration as N₂O with uptakes of -0.36 (-2.7 – 0.40) gN ha^-1 day^-1. Overall, mangroves in the Moresby estuary are fixing some N in their standing litter while removing NO₃ and NH₄⁺ from the water column through denitrification and anammox, temporarily storing N as woody biomass, and accumulating particulate N in their sediments. These mangroves are also functioning as sinks of N₂O. Thus, the protection and restoration of these mangroves provide water quality and climate benefits.