This study reports the hydrodynamics of the transport of suspended particulate matter (SPM) in the Jaguaribe River estuary, which receives the runoff from the largest drainage basin in the state of Ceará, Brazil. The estuary is located in the semiarid region of Brazil, where rainfall occurs primarily between January and May and results in water flow rates exceeding 3000 m3s−1. The drainage basin contains more than 4000 dams, which, during the dry season, block most of the flow of freshwater and sediment. The net balance and transport of sediments were calculated for the wet and dry seasons considering a tidal cycle of 13 h at the interfaces between the upper and middle estuary and between the middle and lower estuary. The Jaguaribe River estuary is classified as partially mixed with weak vertical stratification and a tendency toward being well mixed. The SPM transported during the rainy season originates in the drainage basin due to high river inflow, whereas during the dry season, resuspension and hydraulic fills generated by tides causes the accumulation of SPM in the middle estuary, forming a zone of maximum turbidity. The transport of salt in the estuary was predominantly caused by gravity flow and tidal propagation.