There is no methodology or steps to follow. Infrastructure is needed. In many countries, rivers prone to floods are often carefully managed. Defences such as levees, bunds, reservoirs, and weirs are used to prevent rivers from bursting their banks. When these defences fail, emergency measures such as sandbags or portable inflatable tubes are used. Coastal flooding has been addressed in Europe and the Americas with coastal defences, such as sea walls, beach nourishment, and barrier islands. A dike is another method of flood protection. A dike lowers the risk of having floods compared to other methods. It can help prevent damage; however it is better to combine dikes with other flood control methods to reduce the risk of a collapsed dike. A weir, also known as a lowhead dam, is most often used to create millponds, but on the Humber River in Toronto, a weir was built near Raymore Drive to prevent a recurrence of the flooding caused by Hurricane Hazel in 1954, which destroyed nearly two fifths of the street.
This is a good problem for your local hydrologists and geomorphologists. The flooding may be natural or affected by channel aggradation due to excess sediment from severe erosion upstream within watershed. It is possible to deepen a river, but this may not last, and can cause a base level shift affecting upstream areas. In sandy channel bottoms, avulsion and upstream gullying are possible. Braided streams are an indicator of excess sediment, and it takes a strong vegetation component to stabilize them (anastomosed). Channelization of rivers often causes effects and continuing needs for maintenance, and especially so when frequent flooding is mentioned that suggests a braided system or a system where channel aggradation has occurred, thus reducing the capacity of bankfull channel, which floods on average every year or two. If frequent flooding term used means every year or two, the channel system may be in balance.
Deepening of a coastal river to ocean can increase salt water influence upstream. In some instances, installing J hooks or cross vanes can reduce bank stress, allow for deepening of thalweg, provide grade control and help move sediment to reverse aggradation.