In coastal aquifers, significant vertical hydraulic gradients are formed where fresh water and underlying salt water discharge together upward to the seafloor. Monitoring boreholes may act as "short circuits" along these vertical gradients, connecting between the higher and the lower hydraulic head zones. When a sea tide is introduced, the fluctuations of both the water table and the depth of the mixing zone are also biased due to this effect. This problem is intensified in places of long-screen monitoring boreholes, which are common in many places in the world. For example, all approximately 500 boreholes of the fresh water-salt water mixing zone in the coastal aquifer of Israel are installed with 10 to 50 m long screens. We present field measurements of these fluctuations, along with a three-dimensional numerical model. We find that the in-well fluctuation magnitude of the mixing zone is an order of magnitude larger than that in the porous media of the actual aquifer. The primary parameters that affect the magnitude of this bias are the anisotropy of the aquifer conductivity and the borehole hydraulic parameters. With no sea tide, borehole interference is higher for the anisotropic case because the vertical hydraulic gradients are high. When tides are introduced, the amplitude of the mixing zone fluctuation is higher for the isotropic case because the overall effective hydraulic conductivity is greater than the conductivity in the anisotropic case. In the aquifer, the fresh water-salt water mixing zone fluctuations are dampened, and tens of meters inland from the shoreline, the fluctuations are on the order of few centimeters.