The invasive aquatic plant Egeria densa (Brazilian waterweed) is a submersed aquatic plant that has expanded its distribution in both its native and introduced range. Because the plant grows so densely, it can become a problem for management of waterways and habitat restoration projects. It is difficult to remove once established and mechanical and chemical controls have shown limited effectiveness. Here we analyze the distribution of E. densa in the Sacramento–San Joaquin Delta (the Delta) of California, USA, using environmental variables that include mean water velocity, mean water turbidity, and water column depth. We found that increasing water column depth strongly limited E. densa occurrence, especially when depth at mean lower low water (MLLW) exceeds 2 m. The highest probability of occurrence occurred at locations with a water column depth of −1 to 2 m at MLLW. Turbidity had a reliably negative effect on E. densa occurrence; as water clarity has increased in the Delta, it has likely favored the spread of the plant. Neither mean water velocity nor maximum water velocity had a reliable effect on E. densa probability, in spite of scientific and observational evidence that it is sensitive to flows. These results suggest potentially serious problems with restoration projects that emphasize shallow water habitat in the range favored by E. densa. Without some way to manage spread of the plant—through spraying, sediment loading, or gating—channels in such projects are at risk of being taken over by E. densa. However, these results should be interpreted in light of the fact that water outflow in water year 2008 was very low, and that E. densa abundance may be partially controlled by higher water flows than those considered here.