This study was conducted in two eutrophic shallow lakes (Lake Honda LH and Lake Nueva LN) that share geographic proximity but have contrasting hydrology, meteorology, biogeochemistry, and geomorphology. Our objective was to explore the inter-annual, seasonal, and daily variability in selected biological, physical, and chemical variables of these two systems. Although the study lakes demonstrated a notable inter-annual and seasonal variation in nutrient concentrations, water transparency was the only variable that was consistently more variable in LH than LN. The reason for the greater temporal variability in water transparency of LH is its major susceptibility to wind and rain events. The impact of wind events in this lake is favored by its shallowness and by its silty surface sediment; the high ratio of catchment area to lake area is responsible for the relatively higher susceptibility of LH to rain events than LN. By contrast, in the younger and deeper LN, ground-water discharge buffers certain water chemistry parameters such as conductivity, turbidity, and alkalinity. Interestingly, differences in turbidity and ground-water discharge do not seem to affect the variability in nutrient concentrations, which was similar between the lakes, although these factors may explain differences between the lakes in nutrient concentrations. This paper reveals that the unpredictability and frequency of events in Mediterranean aquatic ecosystems makes it necessary to increase data collection frequency to obtain more accurate simulations in water quality models.