Hundreds gathered in Manila to denounce budget cuts, delayed infrastructure projects and alleged corruption, with both faculty members and activist groups joining the demonstrations.
The protest came days after two senators were accused of receiving kickbacks linked to flood-control projects during a televised congressional inquiry.
Several construction executives also testified in a separate Senate hearing, claiming they were asked for payments worth a quarter of project costs in exchange for government contracts.
The scandal has already forced the resignation of the public works secretary and led Marcos Jr to announce an independent commission of inquiry.
Funding for flood-control projects next year has been suspended, while church leaders, former officials and business groups issued a joint statement condemning the corruption and warning of its impact on a country regularly struck by deadly storms.