Foraminifera, grain size, and carbon and nitrogen isotope ratios and abundances were analyzed in surface-sediment samples collected from three floating fish-cage complexes to address how aquaculture has influenced the Setiu estuary and lagoon of northeast peninsular Malaysia. Two currently active floating fish-cage complexes, SET11-S43 and SET11-S40, are located in the semi-enclosed Setiu lagoon, within four km of an inlet connecting to the South China Sea. The sampling areas experience salinities in the 20s, and sediments have mixed agglutinated and calcareous foraminiferal [total] assemblages, generally dominated by Ammonia aff. A. aoteana and Ammobaculites exiguus. The majority of live foraminifera at these sites belong to agglutinated species; percent of live specimens is greater around the SET11-S43 fish-cage complex, likely related to the presence of aquaculture-related organic-rich mud. Percent agglutinated specimens in total assemblages (live + dead) decrease towards the inlet as total assemblage density and diversity increase due to increased salinity. At a recently (1–3 years) abandoned fish-cage complex, SET11-S9A, located in a low salinity (<5) estuarine setting, Miliammina fusca and Am. exiguus dominate total assemblages.

Surface-sediment grain-size data indicate that fish-cage-related organic-rich mud underlies SET11-S43 and extends tens of meters to the north with a surrounding sandier substrate, typical of most of the Setiu estuary and lagoon system. SET11-S40 is underlain by generally sandy sediment; organic-rich mud characterizes the lagoon immediately to the north of this fish-cage complex. Percent carbon and nitrogen in sediment exhibit distributional patterns that strongly correlate with the distribution of fish-cage mud. Greater amounts of mud, carbon, and nitrogen in sediment are found to the north of the active lagoonal fish-cage complexes. The δ13C and δ13N signatures of the organic matter in this area are attributed to input from the surrounding mangrove forest, whereas their distribution is a result of the interaction of tidal currents with the physical presence of fish-farm complexes. The environmental influence of the active fish cages at lagoonal site SET11-S40 is minimal as a result of the flushing effects of tidal currents from a nearby inlet. Further north at the SET11-S43 lagoonal fish-cage complex, which receives less marine influence (lower salinity and reduced tidal currents), organic-rich mud has accumulated beneath and to the north of the complex. Foraminiferal and sedimentological data from abandoned estuarine fish-farm complex SET11-S9A are indistinguishable from those of adjacent estuarine sites indicating a rapid return to pre-fish-farm conditions following abandonment.

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