The contribution of diffuse nutrient exports from forests to downstream water bodies is significant owing to their extensive spatial distribution across watersheds. However, the intricacies of coupling mechanism between diffuse nutrient exports and meteorological factors driving downstream eutrophication remain poorly understood. Multiple methods involving field sampling, laboratory analysis, and model simulation were utilized to investigate the impact of diffuse nutrient exports from tropical forests on chlorophyll a concentration dynamic in the downstream reservoir. A strong positive correlation was observed between air temperature and chlorophyll a concentration, indicating the direct influence of climatic factors on microalgal biomass. The significant positive linear relationship was also observed between diffuse nitrate exports and chlorophyll a concentration, with a regression coefficient of 0.36 (P < 0.001), underscoring the role of nitrogen inputs in stimulating microalgal growth. The interplay between diffuse nitrate exports and meteorological factors was shown to regulate chlorophyll a concentration fluctuation. Additionally, the structural equation model revealed that increasing temperature and decreasing precipitation could elevate chlorophyll a concentration by enhancing nitrogen availability. Monte Carlo simulation results further revealed that temperature and precipitation were the most influential factors affecting chlorophyll a concentration during dry and rainy seasons, with sensitivity values of 0.94 and − 0.76, respectively. Notably, the eutrophication status was projected to deteriorate from light to moderate under diminishing precipitation conditions. These findings underscore the urgency of addressing eutrophication risks in reservoirs surrounded by tropical forests and the implementation of effective nitrate mitigation strategies is imperative, which offers theoretical guidance for the management of eutrophic water restoration within tropical rainforest regions under changing climate conditions.