Foraminiferal assemblages, sediments, and δ13C, δ15N, and C:N ratios are used to investigate how aquaculture in the Setiu estuarine-lagoonal system (SEL) in Terengganu, Malaysia has affected environmental quality since the mid-1970s. Three cores were collected beneath floating fish-cage sites, two (S43 and S40) from the lagoon and one (S9A) from the estuary. The δ13C and δ15N signatures of core sediment indicate terrestrial sources for organic matter, including mangrove vegetation, throughout the cores. Percent carbon, percent nitrogen, and percent mud increase up core throughout S43. In S40, a similar up-core increase reverses, possibly related to the northward migration of an inlet to a more proximal position. In core S9A a similar reversal in these measurements corresponds to recent abandonment of fish cages at this location.

Foraminiferal assemblages in cores S43 and S40 are dominated by calcareous taxa, in particular Ammonia aff. A. aoteana and Rosalina globularis. Agglutinated specimens, particularly of Ammobaculites exiguus, increase in abundance near the top of S43 and S40, likely in response to an increase in organic matter. Core S9A contains only agglutinated foraminifera, with Trochammina amnicola, Ammotium directum, Am. exiguus, and Miliammina fusca as the most abundant species. Foraminiferal assemblages do not change at sharp boundaries between sand and mud units in S9A, where T. amnicola dominates assemblages throughout the core except in the uppermost 4 cm. This is likely due to taphonomic loss of the delicate M. fusca down core. The percent of live specimens is relatively low in all three cores. The densities of dead foraminifera at S43 and S40 are extremely high at the base of the cores (i.e., at the onset of aquaculture) and near the surface of S40. These high densities are attributed to a baffling effect created by the fish cages as tidal currents transport sediments northwards in the lagoon.

Aquaculture has affected organic-matter content, sediment characteristics, and foraminiferal distributions in the SEL. However, rapid return (probably within one–three years) to pre-aquaculture conditions after the abandonment of S9A and a slower return to pre-aquaculture conditions in S40 suggest that environmental health of the SEL is not overly compromised by the current scale of floating fish-cage aquaculture, particularly where significant tidal flushing occurs.

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