Despite the archaeological importance of Aqua Virgo, a Roman aqueduct built in 19 BC and still functioning nowadays, there is a lack of information about the mortars coming from the inner duct. This work aims to investigate the mortars from Aqua Virgo and Aqueduct Y, an unidentified aqueduct running under the first one in the La Rinascente area (between Via del Nazareno and Via dei Due Macelli, Rome, IT) through Optical Microscopy (OM), X-ray Powder Diffraction (XRPD) and Scanning Electron Microscopy with Energy Dispersive Spectroscopy (SEM-EDS). The aim is to understand which materials guarantee such longevity and differentiate between different intervention phases. Local natural materials with pozzolanic behaviour—in particular, Pozzolane Rosse—and ceramic fragments are widely employed, mixed or not, for the realisation of the hydraulic mortars under investigation, independently of the intervention phase. Of particular interest is the discovery of an amorphous binder composed of Si, Al, Ca, K and Mg in some samples characterised by the absence of calcite.