Salt intrusion in surface waters endangers freshwater availability, influences water quality, and affects estuarine ecosystem services with high economic and social values. Salt transport and the resulting salinity distributions result from the non-linear interactions between salt and water dynamics. Estuaries are often considered under (quasi)-steady assumption or by focusing on specific timescales. Our understanding of their temporal multiscale response to transient forcing is limited, which hinders the implementation of effective mitigation strategies. We apply wavelet analyses to quantify the variability of salt intrusion from hourly to seasonal timescales and unravel the temporal variability of its response across scales. We focus on an estuary that undergoes significant transient forcing, the Modaomen estuary in the Pearl River Delta, and apply the wavelet analyses to year-long data generated by a coastal ocean numerical model. Our results show that this estuary responds to changes in tidal and riverine forcing throughout the year over interwoven timescales. Our results highlight the temporal variability of the salt intrusion response time both within a given regime and for the transition between regimes. They also suggest that tides control the response time more strongly than river discharge, even though river discharge determines the magnitude of the salt intrusion, and thus modulates the evolution of the salt intrusion response time. We propose a broadly applicable framework to calculate response times with simple data. These results can provide a first-order guidance for design and implementation of estuarine management strategies and mitigation measures that ensure water access and facilitate sustainable development.