Farm ponds can be constructed and maintained to improve biodiversity and ecosystem functions in agricultural landscapes. Understanding the initial establishment process of vegetation in different water depths and effects of initial planting on this process is important for pond restoration. In the present study, two experimental farm ponds with or without initial planting were monitored for 5 years after their construction. These two ponds maintained high nutrients over 5 years from the beginning. The unplanted pond showed a rapid vegetation establishment and had more species and higher percent vegetation cover in 2–3 years than the reference pond. Planting accelerated this process by 1 year. Most of the early established species appeared to have originated from seed banks and/or seed rains. The species and functional diversity tended to decrease consistently since pond construction in the planted pond but increase initially and then decrease in the unplanted pond. The time when species composition between the unplanted pond and the planted pond became similar was delayed with the increase of water depth. Four years after pond construction, species composition was similar between the two ponds at all water depths. These results suggest that vegetation can establish quickly in farm ponds with fertile conditions and abundant seed sources through natural recolonization. The restoration approach for a farm pond should be decided considering the allowed time to success and the water depth. If the main goal of farm pond restoration is to improve species diversity, management practices may be more important than planting.