Coastal upwelling is one of the best studied oceanographic phenomena because of its effects on primary production. The western coast of the Iberian Peninsula has high biological diversity, mainly due to this primary production. In this study, the response of salinity and temperature to the occurrence of upwelling was analysed at the Ria de Vigo– and Ria de Aveiro–ocean boundary over the course of a year. Both systems were influenced by similar external forcing, but the response of thermohaline properties differed. Salinity and temperature were dependent on external forcing throughout the water column at Ria de Aveiro, whereas near-bed measurements revealed the presence of upwelled water at Ria de Vigo. Eastern North Atlantic Central Water was observed during spring–summer (summer) at the southern (northern) mouth of Ria de Vigo, but it was not observed at Ria de Aveiro. This difference may be due to the shallowness and narrowness of the Ria de Aveiro mouth, which can limit the entrance of ocean water. The trends found are unlikely to be unique, suggesting that geomorphologic characteristics of system–ocean boundaries determine how physical processes occurring in adjacent coastal areas impact estuarine properties.