The science of forests and floods is embroiled in conflict and is in urgent need of reevaluation in light of changing climates, insect epidemics, logging, and deforestation worldwide. Here we show how an inappropriate pairing of floods by meteorological input in analysis of covariance (ANCOVA) and analysis of variance (ANOVA), statistical tests used extensively for evaluating the effects of forest harvesting on floods smaller and larger than an average event, leads to incorrect estimates of changes in flood magnitude because neither the tests nor the pairing account for changes in flood frequency. We also illustrate how ANCOVA and ANOVA, originally designed for detecting changes in means, do not account for any forest harvesting induced change in variance and its critical effects on the frequency and magnitude of larger floods. The outcomes of numerous studies, which applied ANCOVA and ANOVA inappropriately, are based on logical fallacies and have contributed to an ever widening disparity between science, public perception, and often land-management policies for decades. We demonstrate how only an approach that pairs floods by similar frequency, well established in other disciplines, can evaluate the effects of forest harvesting on the inextricably linked magnitude and frequency of floods. We call for a reevaluation of past studies and the century-old, preconceived, and indefensible paradigm that shaped our scientific perception of the relation between forests, floods, and the biophysical environment.