Berm breaching of intermittently closed estuaries, either naturally or due to management practices, results in a physicochemical disturbance due to the flushing of water, material and biota into the ocean and the subsequent tidal influx. In 2007 and 2008 comparative and controlled studies were employed in three New Zealand estuaries: Sawmill Creek (46°04′S 170°12′E), Otokia Creek (45°57′S 179°20′E) and Kaikorai Lagoon (45°56′S 170°23′E), to investigate the impact of berm breaching on the hyperbenthic macroinvertebrate community in intermittently closed estuaries. Significant changes in community structure occurred in both the weekly comparative and the controlled studies (ANOSIM P<0.01). Furthermore, the catch per unit effort of both total and key invertebrate taxa significantly increased after breaching (ANOVA P<0.01). However, substantial numbers of individuals were expelled into the ocean (5,800 individuals, 20-min sample) while new taxa immigrated into the estuaries. Along with migration-related changes to community structure, berm breaches also resulted in the loss of ∼80% of inundated habitat and the concentration of existing populations. Consequently, the management of intermittent estuary connections to the ocean has implications for the ecology of individual, managed estuaries and also for regional coastal populations of epibenthic invertebrates.