We study salinity in estuaries consisting of a network of channels. To this end, we develop a model that computes the flow and salinity in such systems. We use the model to quantify the mechanisms by which salt is transported into estuarine networks, the response to changes in river discharge, and the impact of depth changes. Results show that when changing the depth of channels, the effects on salt intrusion into other channels in the network can be larger than the effect on the channel itself.