The Loire River watershed accounts for a fifth of metropolitan France. Nevertheless, knowledge of past floods of the Loire River and its tributaries is still very limited. This study aimed to carry out an unprecedented census of floods in the Loire River, during the Little Ice Age (LIA), from the 14th century to the mid-19th century, in order to detect periods of high and low hydrological activity. The abundant historical archives in the cities of Nevers and Decize, as well as other archives consulted, enabled us to record 303 flood events, including 220 in the study area between Digoin and Nevers in Burgundy. This census is heterogeneous over the centuries, with the majority of newly recorded flood events taking place during the 14th and 15th centuries, first half of the 16th century, and 18th and 19th centuries. The use of two types of flood indexes enabled this study to overcome the documentary bias, and detect several decadal periods of high or low hydrological activity during the LIA in the Loire River. Almost all these periods can be found on other rivers in both France and Europe, the Loire River being exposed to the confluence of several climatic influences, as confirmed by comparisons with the North Atlantic Oscillation (NAO), Grand Solar minima and temperature fluctuations. Nevertheless, the coldest periods of the LIA, coupled with negative NAO positions, correspond to periods of high hydrological activity in the Loire River. The study of flood seasonality also reveals a high degree of variability during the LIA, with a higher proportion of flood events occurring in summer and autumn compared with the current seasonal pattern.