Freshwater phytoplankton blooms are increasing in frequency worldwide and regularly put potable water resources, critical to human welfare, in jeopardy. Much more information is needed to effectively predict and mitigate these blooms. Prior studies have highlighted the roles played by both biological factors and physical ones (e.g., hydrodynamics, temperature, precipitation) in bloom formation. Most comprehensive studies have been limited to the temperate zone in Europe, China or North America; the dynamics of tropical and sub-tropical reservoirs are less well-characterised. Numerous studies have highlighted the relationship between phytoplankton and temperature or precipitation, but few have focused on the temporal scale of these relationships. This work evaluates the water quality of 155 freshwater reservoirs in Ceara state in northeast Brazil. We propose weather and climate conditions as natural drivers for changes in chlorophyll-a, cyanobacteria, total phosphorus and total nitrogen concentrations, that we consider as water quality parameters. We hypothesise that links between water quality and temperature and precipitation strongly depend on the timescale considered. Additionally, we propose a statistical definition, based on percentile thresholds, of extremes events in water quality, a criterion that has been lacking for the study of freshwater algal blooms and that will enable new regional and global comparisons. We aim to explore the potential links between extremes in water quality in tropical freshwater bodies of Ceara their predictors, by applying a multitemporal scale approach and discriminating the impact of the daily weather fluctuations from interannual climate variability. We find that water quality in Ceara is frequently below international standards, representing a threat for human and animal welfare. Reservoirs’ water level was a key predictor of bloom occurrence, thus linking low annual accumulated precipitation to inferior water quality. At the daily scale, high temperature promotes bloom formation during periods of drought. These findings suggest enhanced precautions during dry periods when the reservoirs are most prone to algal blooms, which can aggravate the drinking water scarcity in these years.