Many mangroves were forced to act as informal pollution mitigation zones and double up as conservation areas. Long-term data are presented for a high-profile mangrove reserve acting as such a mitigation zone in urban Thailand. Efficient mineralization of organic wastes by mangrove soil in a semi-engineered and hydraulically contained zone made it possible not to compromise the reserve's natural status. The data demonstrate that the treatment zone could process organic waste with an eight-fold efficiency in comparison to previous reports. Clones of microbial taxa critically novel for mangrove ecosystems were recovered (anammox bacteria and archaeal ammonia oxidizers), suggesting their significant presence. Community structures of nitrogen-cycling and other taxa of natural and hypernutrified soils did not differ substantially. It is suggested that waste nitrogen removal may have occurred through bacterial and archaeal nitrification, conventional denitrification and anammox process. The article addresses the issue of multi-functional use of ever-shrinking habitats available for wildlife conservation. Data on key microbial, floral and faunal communities demonstrate that the mangrove exhibited stability under the major nutrient load. Supply of additional nutrients correlated with an enhancement of mangrove growth and diversity of selected key invertebrates/vertebrates which increase conservation potential of the reserve. Serving to determine ecologically safe nutrification limits, the study suggests that a successful rehabilitation of an urban mangrove to its near-natural status is feasible.