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Lakes provide essential supporting services, making sustained monitoring studies crucial amid rising environmental stressors, which are absent in mountain lake research. To fill this gap, this study assessed surface water quality in protected lakes – Balinsasayao and Danao – in the Philippines, using data collected from 2021 to 2024 across dry (March) and wet (August–November) seasons. Temporal (interannual and seasonal) variability was analysed using Generalised Additive Mixed Models (GAMMs) and Principal Component Analysis (PCA). Results showed that temperature, coliform, and chemical parameters significantly fluctuated interannually, indicating that water quality over long years had been shaped by internal processes, catchment inputs, and climate-driven warming. Seasonal analyses revealed rainfall affects pH and dissolved oxygen dynamics. PCA Dimension 1 (38.8% variance) reflected a negative correlation between temperature and positively intercorrelated variables, including TSS, coliform, pH, colour, and rainfall, while Dimension 2 (24.4% variance) separated samples by inorganic nutrients versus organic load indicators, highlighting the physical–chemical factors and nutrient effects on water quality. Findings show climate vulnerabilities in tropical mountain lakes, urging integrated management to safeguard biodiversity and sustain the wide range of supporting services these systems provide.