This study explores: (1) whether the abundance of macroinvertebrates differs between macrophytes differing in both morphological complexity and tolerance to nutrient enrichment; (2) whether the distribution of invertebrates between macrophytes is due to active habitat choice; and (3) whether invertebrates prefer structurally complex to simple macrophytes. Macroinvertebrate abundance was compared between two common soft-bottom plants in the Baltic Sea that are tolerant to eutrophication, Myriophyllum spicatum and Potamogeton pectinatus, and one common plant that is sensitive to eutrophication, Chara baltica. Both field sampling and habitat choice experiments were conducted. We recorded higher total macroinvertebrate abundance on the structurally complex M. spicatum than on the more simply structured P. pectinatus and C. baltica, but found no difference in macroinvertebrate abundance between P. pectinatus and C. baltica. In accordance with the field results, our experiment indicated that the crustacean Gammarus oceanicus actively chose M. spicatum over the other macrophytes. Besides, we found that G. oceanicus actively preferred complex to simply structured artificial plants, indicating that the animal distribution was at least partly driven by differences in morphological complexity between plant species. In contrast, the gastropod Theodoxus fluviatilis did not make an active habitat choice between the plants. Our findings suggest that human-induced changes in vegetation composition can affect the faunal community. Increased abundance of structurally complex macrophytes, for example, M. spicatum, can result in increased abundance of macroinvertebrates, particularly mobile arthropods that may actively choose a more structurally complex macrophyte.