Previous studies show that the fuzzy-based approach predicts incoming floods better than machine learning (ML). However, with numerous observation points, difficulties in manually determining fuzzy rules and membership values increase. This research proposes a novel fuzzy logic-based learning (FLBL) that embeds missing data imputations and a fuzzy rule optimization strategy to enhance ML performance while still benefiting from fuzzy theory. The simple moving average handles sensors’ missing data. The logical mapping is used for fuzzification automation and fuzzy rule generation. The join function between the Szymkiewicz–Simpson coefficient similarity and max function is applied to optimize a fuzzy rules model. The case study uses observation data from three rivers traversing three districts in Semarang City. As a result, FLBL achieves 97.87% accuracy in predicting flood, outperforming the decision tree (96%) and the neural network (73.07%). This work is significant as a part of preventive flood-related disaster plans.