Mangroves play an important role in the storage of carbon (C) and nitrogen (N) within estuarine systems, yet are being lost at an alarming rate throughout the tropics. In contrast, temperate mangroves have increased in area at many locations in recent decades. Field surveys, sediment sampling, allometry, and C and N analysis were used to determine total C and N stocks in five temperate Avicennia marina subsp. australasica forests in New Zealand. This is the first study developing allometric functions to estimate root biomass C and N stocks for A. marina. A. marina forests stored 117.1 ± 16.8 t C ha −1 and 15.4 ± 1.0 t N ha −1 in above and below-ground biomass and sediment to 100 cm depth. Below-ground biomass and sediment C and N stocks contributed 88 ± 3 and 99 ± 0.4% to total C and N stocks, respectively, emphasizing the importance of below-ground biomass and sediment in mangrove ecosystems. The results of this study can be used to inform management decisions for estuarine and coastal ecosystems, currently undergoing rapid changes in mangrove area.