Due to their dimensions, small and shallow water bodies are more sensitive to changes in nutrient load, water flow, and human management. The four water bodies studied are small (area <0.01 km²), constantly supplied by a non-anthropogenic source of nutrients, and these water bodies present different trophic states: mesotrophic, eutrophic, and hyper-eutrophic. The objective of this study was to identify the key environmental factors that created differences in the trophic state of these adjacent shallow urban lakes by modeling chlorophyll-a (Chl a) through the application of the Partial Least Squares Regression (PLSR). The models (n = 36) explain 45.8–60.6% (R²), and predicts 39–52.9% (Q²) of the variance. Environmental variables were identified in the water bodies as critical factors of trophic state determination, water residence time (WRT), ions (e.g., Ca²⁺), and minerals as hydroxyapatite (HAP). These variables were related to processes that could improve trophic conditions, such as flushing and phosphorous precipitation. Conversely, N-NH₃ concentration was associated with nutrient recycling, and found to be able to promote eutrophication.