Gammarus lacustris and Hyalella azteca (hereafter G. lacustris and H. azteca, respectively) are important components of secondary production in wetlands and shallow lakes of the upper Midwest, USA. Within the past 50 years, amphipod densities have decreased while occurrences of fish and intensity of agricultural land use have increased markedly across this landscape. We investigated influences of fish, sedimentation, and submerged aquatic vegetation (SAV) on densities of G. lacustris and H. azteca in semipermanent and permanent wetlands and shallow lakes (n = 283) throughout seven eco-physiographic regions of Iowa, Minnesota, and North Dakota during 2004–2005. G. lacustris and H. azteca densities were positively correlated with densities of SAV (P < 0.001 and P < 0.001, respectively). Both species were negatively correlated with densities of large fish (non-Cyprinidae; P = 0.01 and P = 0.013, respectively) and with high densities of fathead minnows (Pimephales promelas; P < 0.001 and P = 0.033, respectively). H. azteca densities also were negatively correlated with densities of small fish (e.g., other minnows [Cyprinidae] and sticklebacks [Gasterosteidae]; P = 0.048) and common carp (Cyprinus spp.; P = 0.022). G. lacustris densities were negatively correlated with high levels of suspended solids (an index for sedimentation; P < 0.001). H. azteca densities were positively correlated with the width of upland-vegetation buffers (P = 0.004). Our results indicate that sedimentation and fish reduce amphipod densities and may contribute to the current low densities of amphipods in the upper Midwest. Thus, removing/excluding fish, and providing a thick buffer of upland vegetation around wetlands may help restore amphipod densities and wetland and water quality within this landscape.