El Yali coastal reserve is the most important wetland complex in Mediterranean climate central Chile, especially due to the native and foreign bird fauna which arrives here periodically. The coastal lagoon, part of a micro-tidal estuary (1.2 m tidal range), is a shallow (<1 m depth) dynamic system and unique site of coexistence of northern halophyte and southern palustrian riparian vegetation. This study identifies and quantifies the effect of forcing variables in the lagoon water level over I year of data collection. Transects of piezometers with level sensors were installed between the coastal lagoon and the sea. Monthly water quality data were collected. During the winter rainy season, the lagoon connects with the sea via an ephemeral tidal inlet, producing noticeable daily variations in the water level, up to 80-cm depending on the tides. In contrast, during the season when bar closure of the inlet disconnects the lagoon from the sea, the lagoon level is very stable and only decreases very slowly due to evaporation, which also makes the system hypersaline. During the connection phase, analyses using general pattern, spectral and Fourier analysis of the sea-vs. lagoon-level signals show that two temporal scale hierarchies are relevant: monthly (due to moon cycles) and daily (due to tidal cycles every 12.5 and 24.2-h). A simple diffusion numerical model simulated the water table trends well for the sand bar between the lagoon and the sea, supporting the main effect of the sea level on the lagoon water levels.