The devastating impact of flooding on aquaculture-based businesses has been a topical issue in recent workshops and other public discussions in Nigeria. The survival and growth of aquaculture businesses depend on the profit earned by the operators. Empirical information on the relationship between floods and profitability is scarce. This study examines the relationship between floods and economic returns for fish farmers in Rivers State, Nigeria. This research derives its importance from its relevance to improving flood mitigation strategies among fish farmers. The study used questionnaires, focus group discussions, and personal interviews to generate data for the study. About 92 fish farmers were randomly sampled for the study. Descriptive and inferential statistics were used for data analysis. Descriptive statistics (probability, percentage, and frequency distribution tables) and inferential statistics (binary logistics regression and multiple regression model) were used. The frequency/severity of floods is statistically significant (P ≤ 0.05). The R2 value of 0.6403 (64%) indicates that flooding explains a 64% variation in the profit earned by fish farmers in Rivers State, Nigeria. The result of this study also showed that educational level, income, membership in an association, and frequency of extension contacts are the factors that influence a fish farmer’s willingness to pay for improved flood management preferences. We found sufficient evidence to conclude that effective flood management strategies increase the profit earned by fish farmers.