Anthropogenic activities are altering flood frequency-magnitude distributions along many of the world's large rivers. Yet isolating the impact of any single factor amongst the multitudes of competing anthropogenic drivers is a persistent challenge. The Usumacinta River in southeastern Mexico provides an opportunity to study the anthropogenic driver of tropical forest conversion in isolation, as the long meteorological and discharge records capture the river's response to large-scale agricultural expansion without interference from development activities such as dams or channel modifications. We analyse continuous daily time series of precipitation, temperature, and discharge to identify long-term trends, and employ a novel approach to disentangle the signal of deforestation by normalising daily discharges by 90-day mean precipitation volumes from the contributing area in order to account for climatic variability. We also identify an anthropogenic signature of tropical forest conversion at the intra-annual scale, reproduce this signal using a distributed hydrological model (VMOD), and demonstrate that the continued conversion of tropical forest to agricultural land use will further exacerbate large-scale flooding. We find statistically significant increasing trends in annual minimum, mean, and maximum discharges that are not evident in either precipitation or temperature records, with mean monthly discharges increasing between 7% and 75% in the past decades. Model results demonstrate that forest cover loss is responsible for raising the 10-year return peak discharge by 25%, while the total conversion of forest to agricultural use would result in an additional 18% rise. These findings highlight the need for an integrated basin-wide approach to land management that considers the impacts of agricultural expansion on increased flood prevalence, and the economic and social costs involved.