An automatic and modular system for handling trays (32) used for containing plants or the like to be grown through hydroponic, or aeroponic, or aquaponic farming, comprises a first module (30) with a quadrangular plan and a vertical arrangement delimited by respective vertical supports (31), said first module (30) comprising two lateral zones, each of which includes a plurality of substantially horizontal and overlapping supporting seats or guides (37, 37′;) for trays (32), and a central zone in which a vertical tray transfer device (33) operates, slidably along a vertical axis (Z) arranged on a movement means activated by motorization assemblies (34) able to translate said vertical transfer device (33) from a lowered position to a raised position for bringing itself to each tray (32) and vice versa, said vertical transfer device (33) being provided with a resting shelf (33′;) for a tray (32) and with a first means adapted to translate along a first horizontal axis (Y) said tray from and towards a respective seat provided inside one of said lateral zones. Said first module (30) further comprises a second means (36) arranged in said central zone in which said elevator device (33) operates, adapted to take in charge a tray (32) when the latter is located on the shelf (33′;) of said elevator device (33) and to displace said tray (32) along a second axis (X) horizontal and orthogonal to said first horizontal axis (Y) for performing the direct transfer of said tray (32) towards a further shelf (33′;) of a further vertical transfer device (33) of a second module (30) arranged adjacent and connected to said first module.