The physical, chemical, and biological dynamics under changing atmospheric conditions of Laguna Lake, Philippines were analyzed from intensive observations. Diel measurements were conducted for 48 continuous hours for both dry and wet tropical seasons in addition to fine resolution long-term monitoring. Results revealed significant vertical and diel variations of lake variables in spite of a shallow water depth (2.5 m) caused by the intense surface heating from solar irradiance (~800 W m−2) and accentuated by the lake’s high turbidity (16–32 ftu). Late afternoon land-lake breeze (~5–7 m s−1) regularly breaks daytime thermal stratification, and convective cooling at night maintains isothermal condition until dawn of the next day. The stratified condition demonstrated a wind-driven, density-induced 2-layer current pattern with a windward moving epilimnion (~4 folds faster) and a compensating hypolimnetic flow in the general lake circulation direction. Laguna Lake was observed to have a dominating diel cycle but also undergoes significant seasonal limnological variations brought primarily by climate, hydrology, and its interaction with the adjacent sea. Significantly correlated variations of pH, chlorophyll-a and DO in the dry season were indicative of the higher biological activity associated with the intrusion of polluted waters from Metro Manila. The non-occurrence of thermal over-turn was observed to be regularly followed by bottom hypoxic conditions (2–4 mg L−1), indicative of the eutrophic condition of the lake and the importance of diel wind-induced mixing in the bottom supply of DO. Laguna Lake was found to be predominantly net heterotrophic (GPP:R < 1, NEP < 0).