Although destabilization and stabilization of soft sediments by macro-infauna are regarded as key to understanding benthic community dynamics, how component populations are affected concurrently by both agents was poorly investigated. On an intertidal sandflat, Kyushu, Japan during 1979 − 2014 (previous study) and 2015 − 2019, monitoring was made of the populations of the filter-feeding gastropod, Umbonium moniliferum, the burrow-dwelling ghost shrimp, Neotrypaea harmandi (destabilizer), and the tube-building polychaete, Mesochaetopterus minitus (stabilizer). Results revealed that gastropod population changes were driven by an interplay of shrimp, polychaete, and the stingray, Hemitrygon akajei, foraging for shrimp by sediment excavation. The gastropod went through high abundance (1100 m−2) in 1979, extinction during 1986 − 1997, two marked recoveries with peaks in 2001 and 2009, a slight recovery in 2016, and near extinction in 2019. These changes largely followed the fluctuation in shrimp density across a threshold of 160 m−2 inhibiting gastropod recruitment. The polychaete exhibited intermittent outbreaks with peaks in 2000, 2007, and 2016, with maximum densities of 15,000 − 24,000 m−2. Sandflat topography and sedimentary variables were measured during 2015 − 2017. Sediment stabilization by polychaete aggregations at the mid-tidal zone is suggested to have boosted gastropod recruitment. Release at sea and retrieval on shore of drift cards mimicking gastropod larvae with 3- to 9-day planktonic duration was conducted in 2008 − 2009 to specify source populations sending larvae to the present population. Potential source populations were censused in 1998 and 2017 − 2018. Their recent virtual extinction appears responsible for the present population’s decline from 2011. This raises the need for metapopulation perspective to understand local dynamics.