ABSTRACT: Gulf of Mexico estuaries contain an abundance of habitat-forming submerged vegetation that provide various ecosystem services. However, these estuaries now harbor numerous invasive macrophytes, such as Eurasian milfoil Myriophyllum spicatum. Previously, we showed that milfoil gained a foothold in the Mobile-Tensaw Delta, Alabama, USA, in protected waters north of a manmade causeway that significantly reduces wave action. Here, we collected associated organisms using a suction sampler and compared the composition and abundances of fauna residing in M. spicatum and wild celery Vallisneria americana, the most abundant native macrophyte, during day and night. North of the causeway, where water flow is limited, a 5-fold reduction in the abundance of organisms was documented in M. spicatum at night, while abundance in V. americana varied little. We found that this nocturnal decrease was accompanied by changes in community structure in M. spicatum north of the causeway, driven by reductions in invertebrates such as Gammarus amphipods, Neritina snails, and Callinectes sapidus crustaceans. In contrast, communities in V. americana, although distinct from M. spicatum, exhibited little spatial or temporal difference. Subsequent analyses indicated that reduced dissolved oxygen in M. spicatum north of the causeway at night drives assemblage patterns. These results suggest that hydrological alterations exacerbate M. spicatum’s negative effects through the creation of hypoxic zones and that daily migrations into these habitats may be necessary for organisms to garner the benefits of this vegetation. Finally, this work highlights that our understanding of the concomitant impacts of altered hydrology and invasive macrophytes is incomplete without considering diel variability.