Restoration of submerged macrophytes to lake that have lost them can be difficult but can be helped by studies on historical vegetation data and remnant seed banks in the sediments. We analysed sediment seed banks and historical vegetation change data in Lake Dianchi, China, and aimed to develop a possible recovery trajectory of submerged vegetation. The results indicate that phosphorus concentrations have increased by 28 times in the lake since 1961 and macrophytes that used to grow at 5–6.5 m are now confined to water less than 3 m deep. Many species had disappeared by 1978 and a former 17 species and 88% cover in 1961 was reduced to 9 species in three turbidity-tolerant communities with only 2% cover by 2010. The remaining seed bank was dominated by two species, still present in the lake and many former species, which had been very abundant, were not found as seeds. We suggest that macrophytes can be restored to areas shallower than 3 m by using three turbidity-tolerant species, and that other formerly present species will need to be reintroduced when conditions have been further improved.