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 the present study of nutrient flow potentials in the agricultural ecosystem. The study was in line with the previous study at the rainy season of November – February 2012, that limited to the observation of N flows at a farm scale agri-aquaculture system in the tidal swamp land during the dry season of April - July 2015. In combination with the previous study (Kurnain et al., 2012) N-inorganic capacity of the agri-aquaculture system in the tidal swamp land during two rice planting seasons at the rainy season of November – February 2012 and the dry season of April – July 2015 reached 474 kg N ha-1, which is derived from rainwater (IN1), river water (IN2), fertilizer (IN3), and the internal flow of the fishpond muds ( IF1) and rice straw (IF2) respectively 23, 329, 69, 32 and 20 kg N ha-1 (Figure 1). In agro-ecosystems naturally stagnant as swamp lands, input from river water must be balanced with the output in the form of drainage water (Folmer et al., 1998), and therefore the net input of river water through the process of sedimentation is 102 kg N ha-1. Thus the net capacity of the system reached 247 kg N ha-1 can potentially be used for biomass production during the year (Shepherd and Soule, 1998