Schistosomiasis is an endemic, neglected tropical disease in Africa. Nigeria has the highest prevalence and intensity of the infection, with a severe transmission rate. The World Health Organisation (WHO) targeted the interruption of transmission and the elimination of the disease by 2030. However, an increasing climate change consequence, flooding, may foster a challenge in the control of the infection. This article provided an overview of the potentiality of flooding in increasing the spread of schistosomiasis transmission in Nigeria, thus hindering its control. Floods increase the dispersal of Bulinus and Biomphalaria snails, which are the intermediate hosts of schistosomiasis, from active transmission areas to areas without the infection, thereby causing an increase in the transmission of schistosomiasis in humans and animals (especially livestock). The destruction of sanitary facilities in schistosomiasis-infested areas and the displacement of people and animals by flooding increase  the water contact activity of the displaced victims (humans and animals) and the dispersal of Schistosoma eggs that amplify schistosomiasis transmission. There was also the tendency for Schistosoma hybrids from neighboring Niger River Basin (NRB) countries to be established in Nigeria due to floods. Monitoring the dispersal patterns and/or the modeling of water snails (Bulinus and Biomphalaria) in endemic countries like Nigeria and the prevalence of livestock, wildlife, and hybrid schistosomes before and after flooding is strongly recommended in Nigeria for effective control interventions.