Several coral reefs of Nanwan Bay, Taiwan have recently undergone shifts to macroalgal or sea anemone dominance. Thus, a mass-balance trophic model was constructed to analyze the structure and functioning of the food web. The fringing reef model was comprised of 18 compartments, with the highest trophic level of 3.45 for piscivorous fish. Comparative analyses with other reef models demonstrated that Nanwan Bay was similar to reefs with high fishery catches. While coral biomass was not lower, fish biomass was lower than those of reefs with high catches. Consequently, the sums of consumption and respiratory flows and total system throughput were also decreased. The Nanwan Bay model potentially suggests an overfished status in which the mean trophic level of the catch, matter cycling, and trophic transfer efficiency are extremely reduced.

Before 2001, the ecological protection area in the Kenting National Park (KTNP), southern Taiwan, was poorly described. In this study, a set of four-year data (2001-2004) of seawater qualities at 19 sampling sites around the Nanwan Bay in the KTNP was used to explore anthropogenic impacts to ecological environment, especially coral reefs. The parameters of water quality were analyzed immediately after collection. The results showed that higher values of nutrients and suspended solids were attributed to the higher run-off around Nanwan Bay. The fluxes of nutrients and suspended solids were consistently correlated to rainfall. Hence, equations were developed to calculate nutrient fluxes and suspended solids by using only rainfall data. Our results show that suspended solids and ammonia were the dominant factors leading to the drop in coral coverage. In summary, the water quality in the intertidal zone of Nanwan Bay has been degraded and required greater attention.

Tapong Bay, a eutrophic and poorly flushed tropical lagoon, supports intensive oyster culture. Using the Ecopath approach and network analysis, a mass-balanced trophic model was constructed to analyze the structure and matter flows within the food web. The lagoon model is comprised of 18 compartments with the highest trophic level of 3.2 for piscivorous fish. The high pedigree index (0.82) reveals the model to be of high quality. The most-prominent living compartment in terms of matter flow and biomass in the lagoon is cultured oysters and bivalves, respectively. The mixed trophic impacts indicate that phytoplankton and periphyton are the most-influential living compartments in the lagoon. Comparative analyses with the eutrophic and well-flushed Chiku Lagoon and non-eutrophic tropical lagoons show that high nutrient loadings might stimulate the growth and accumulation of phytoplankton and periphyton and therefore support high fishery yields. However, net primary production, total biomass, fishery yields per unit area, and mean transfer efficiency of Tapong Bay were remarkably lower than those of Chiku Lagoon. The lower transfer efficiency likely results from the low mortality of cultured oysters and invasive bivalves from predation or the lower density of benthic feeders constrained by the hypoxic bottom water as a result of poor flushing. This might therefore result in a great proportion of flows to detritus. However, the hypoxic bottom water might further reduce the recycling of the entering detritus back into the food web. In contrast to many estuaries and tropical lagoons, poor flushing of this eutrophic tropical lagoon might induce a shift from detritivory to herbivory in the food web.