Understanding saltwater intrusion processes is crucial for both ecosystem health and water resource management in river estuaries. With the development of the global coastal economy, many estuaries worldwide have undergone shipping engineering constructions. Channel deepening in coastal areas adversely impacts the quality of freshwater required for ecological purposes, human consumption, and agricultural and industrial activities. Many studies have focused on saltwater intrusion processes in artificial canals capable of high and medium runoff characteristics; however, little is known about seawater intrusions in canals with low runoff and ship locks located far away from the estuary. This study focuses on the saltwater intrusion process in such a canal, using the Pinglu Canal of Qinjiang River Estuary in China as a prototype example. A three-dimensional (3D) numerical saltwater intrusion model using the standard k–ε turbulence closure was developed to simulate the saltwater intrusion process pre- and post-canal construction. The verification was conducted by comparing the simulated time series of the tidal level, velocity magnitude, and salinity with observations, and the impact of channel deepening on the saltwater intrusion in the Qinjiang River was analysed based on various numerical experiments. After channel deepening, mixing decreased following the decrease in flow velocity, the saltwater intrusion extent could reach the Youth Ship Lock after an increase of 5 km compared to the extent under natural conditions during high tide, and seawater remained in the channel during ebb tide, with freshwater discharge being Q < 20 m3/s. Furthermore, during the dry season, salinity in the approach channel downstream the Youth Ship Lock exhibited a trend of cumulative increase toward a stable value, and the correlation with the tide range cycle decreased from 0.62 under natural conditions to 0.09, whereas the correlation with the upstream inflow increased from 0.10 under natural conditions to 0.51. Results further indicated that the sensitivity of the saltwater intrusion to the flow rate was at a maximum, and its sensitivity to the tidal range was of minor significance after canal construction. Accordingly, a dimensionless function was constructed to quantify freshwater discharge from the Youth Hydro-hub to reduce the saltwater intrusion under variations in the tidal range and salinity during the low-water discharge period. This study can aid water resource management and suggest methods for mitigating saltwater intrusions in this type of artificial canal. •Salt intrusion process is investigated in an artificial canal with low runoff.•Saltwater intrusion extent can reach the ship lock far away from the estuary.•The sensitivity to water discharge is the strongest downstream the ship lock.•The sensitivity to tidal range decreased as increasing of the distance from estuary.•An empirical function is developed to quantify salinity reduction freshwater.