This study was the first to develop, install and examine a secondary treatment system for domestic wastewater specific to permeable carbonate sand systems. The ‘ecoTrench’ (eT), relied on effluent passing through a number of different treatment layers including a coconut husk humus ecology, a saturated trench and unsaturated carbonate sands. An eT was installed on a residential property on the main island of Rarotonga in the Cook Islands and received primary treated effluent from a septic tank over a 21 month period from May 2009 until February 2011. Nutrient removal efficiencies for the eT averaged 63% of total phosphorous and 43% of total nitrogen. The eT was an effective nitrifyer of NH 4 + to NO 3 − with almost complete attenuation of NH 4 + as effluent passed through the system. Uptake rates of NH 4 + averaged 36.7±4.1mmolm −3 h −1 as wastewaters left the saturated trench. The addition of labelled stable isotope ( 15 NH 4 + ), showed that simultaneous nitrification/denitrification was occurring in both aerobic and anaerobic treatment layers. Elevated concentrations of dissolved organic nitrogen (DON) were seen as effluent left the saturated treatment layer before largely being attenuated as effluent moved down through the sediment profile. This may have contributed to a significant build-up of NO 3 − as effluent moved towards groundwater largely due to inhibited denitrification and the mobilization and remineralisation of previously assimilated DON. The eT represents an efficient and effective way to reduce nutrient loading to groundwater and can work well within the constraints of many island communities based in permeable carbonate sand systems.