In situ seed banks are a promising avenue for restoration of plant communities damaged by anthropogenic changes. The invasive rusty crayfish (Orconectes rusticus) has had well documented effects on macrophytes in north temperate lakes. To understand mechanisms of macrophyte recovery from the seed bank, we examined seed banks from lakes with different durations of exposure to O. rusticus and compared these findings to longterm macrophyte surveys. We cored littoral-zone sediments at sediment depths of 0–5, 5–10, and 10–15 cm to test whether deeper layers hold viable seeds that can be used to restore macrophytes. The seed bank in uninvaded lakes contained a higher number and richness of viable seeds than did the seed bank in invaded lakes. Number and richness of viable seeds decreased with sediment depth in all lake categories, and most seeds were found in the top 10 cm. Among all lakes, at most, 33% of the species recorded in field surveys of standing vegetation were represented in the seed bank. We conclude that the seed bank has only modest potential to contribute to natural recovery. Natural regeneration of the macrophyte community is more likely to rely upon vegetative propagules from remnant stands in invaded lakes, especially from very soft-bottom areas avoided by crayfish. Our results emphasize the importance of preventing destruction of macrophytes, especially in lakes without habitats likely to constitute a refuge for macrophytes.