With the increasing warming of the Arctic, the summertime ice-free period in the coastal Arctic becomes longer and the water exchange between arctic lagoons and coastal Beaufort Sea becomes more important for land–ocean interaction. This study examined the dynamics of water exchange between the arctic lagoons and the Arctic Ocean under the influence of weather systems (the transient arctic cyclones and hovering Beaufort High pressure system). We implemented rare observations, numerical modeling with the Finite Volume Community Ocean Model (FVCOM), and a forcing-response Empirical Orthogonal Function (fr-EOF) analysis to determine the weather-driven flow patterns and characteristics in the micro-tidal arctic lagoon (Elson Lagoon) with little freshwater discharge. The results were validated for both tidal and subtidal currents with in situ data. The inlets of the lagoon were significantly impacted by wind associated with the weather systems and the flows through the inlets were highly correlated with each other. The fr-EOF analysis for the 1.5-month FVCOM output indicated three significant modes of wind-driven flow. In the deepest (~16 m) northwestern-most inlet, a counter-wind flow occurred more than 96% of the time due to setup and set down of water level inside the lagoon and the vorticity balance related to the wind stress and water depth. For about 60–80% of the time, the exchange flow was out of the lagoon through the northwestern-most and deepest inlet due to the strong easterly winds dictated by the Beaufort High; this dominant flow is mainly caused by the persistent easterly wind as a limb of the Beaufort High pressure system, modified by the transient arctic cyclones with a westerly wind and inward flows at the westernmost inlet of Elson Lagoon. This study shows that the alternating influence from the cyclone-anticyclone weather systems produces a meteorological tide in the subtidal spectrum which dominates the water exchange in the region through the multiple inlets. With the observed increase in cyclone strength and frequency under the warming trend, this may imply a greater contribution from the westerly wind because of the increased cyclonic activities. If this is the case, the inward flow might increase and have an effect on sediment, larval, and nutrient transports through this system.