The strategy of sub-optimum land uses including tidal swamp lands through a commodity based approach is difficult to be implemented instead of an agricultural-ecosystem based approach. In line with that is a strategy of fertilization also has to refer to the agricultural ecosystem based approach. To formulate the strategy of fertilization in the tidal swamp land it is necessary to carry out an observation of nutrient flow potentials in the agricultural ecosystem. This preliminary study was limited to the observation of N flows at a farm scale agroaquaculture system in the tidal swamp land during rainy season at November 2011 - January 2012. The total N capacity of the system reached 167 kg ha-1. In the amount of 84 kg ha-1 of the total capacity was available for biomass production in the system, coming from river water,fishpond muds, and rainwater successively 55, 16, and 13 kg N ha-1. Optimizing N flows of the system related to the fertilization strategy could be reached through the development of farm lands into an agro-aquaculture system. With the ratio of land area of raised beds and fishpond of 3:7, the system supplies 31.5 and 36.7 kg N ha-1 in order to produce biomass on raised beds and fishpond respectively.