The Water Framework Directive (WFD) requires European countries to achieve a good ecological status of surface water bodies and demands that River District Authorities define ecological flows consistently. Nevertheless, the relationship between ecological and hydrological indicators is not fully understood and not straightforward to apply because ecological and hydrological indicators are monitored by different institutions, with different timings and purposes. This work examines the correlation between a set of ecological indicators monitored by environmental agencies (STAR-ICMi, LIMeco, IBMR, and TDI) and water levels with assigned durations monitored by the hydrologic service in Tuscany (central Italy). Reference water levels are derived from stage-duration curves obtained by the statistical analysis of daily levels in the same year of ecological sampling. The two datasets are paired through a geospatial association for the same river reach and the correlation is measured through Pearson’s r. The results show poor correlation (r between −0.33 and −0.42) between ecological indicators and hydrologic variables, confirming the findings observed in other Italian catchments with different hydrologic regimes, climate, and anthropogenic pressures. Nevertheless, the negative correlations show a decreasing water quality with water depths, i.e., in the lower part of the catchments more affected by anthropogenic pressures. These findings suggests that the determination of ecological flows with a purely hydrological approach is not sufficient for achieving WFD objectives in the study area.