In order to study the influence of variation of the combined action of runoff and tide on fortnight saline water intrusion distance in the runoff-dominated stratified estuaries, a three-dimensional numerical simulation experiment of stratified salt water movement in a generalized estuary is carried out. The results show that under the condition of constant runoff, the daily maximum intrusion distance of fortnight saline water is shown as a clockwise loop curve with tide difference around the quasi-equilibrium state. The smaller the runoff is, the larger the difference from the quasi equilibrium and the longer the strong intrusion after the neap tide as well as the faster decline. The time-effect of stratified mixing process leads to the nonlinear adjustment of fortnight salt water movement. The saltwater state generally has the characteristics of maximum intrusion occurring 2~3 days after the minimum tide, and minimum intrusion occurring 1~2 days after the maximum tide under the generalized conditions in this paper. According to the basic responses of the salt water movement, the time of increasing flow pressure and suppressing salt intrusion is determined in engineering measures. By increasing the upstream runoff at neap tide and lasting for 7 days to the spring tide, and then taking advantage of the natural decline of fortnight salt water, the obvious effect of suppressing salt intrusion and saving the upstream freshwater resources in the dry season can be achieved.