The large population contingent and the precarious urban planning in the metropolitan region of São Paulo have resulted in uncontrolled growth in areas where springs exist, generating strong pressures on the reservoirs. Concomitantly, a lack of articulation between public and private policy has led to various socio-environmental conflicts in the Billings watershed. This spring, which is responsible for the direct and indirect supply of water to millions of people, represents an enormous challenge for water resource management. In this context, this study aimed to analyze the seasonal limnological conditions of the Billings Complex, in particular the Rio Grande and Taquacetuba branches, and discuss the implications for the management procedure applied in the branches. Physical (water temperature, pH, electrical conductivity, suspended material, organic and inorganic suspended material) chemical (dissolved oxygen, total phosphorus and nitrogen, nitrate, nitrite, ammonium and inorganic phosphorus) and biological (chlorophyll-a) variables of the water were analyzed and the Trophic State Index was calculated. The results indicate a hypertrophic state in the Taquacetuba branch. The Rio Grande branch presented a mesotrophic state which is, however, artificially maintained due to copper sulfate and hydrogen peroxide treatments. The results are also discussed in light of CONAMA Resolution 357/2005. Levels of chlorophyll-a and total phosphorous in the Taquacetuba branch do not conform to the proposed class of use, class I. In this branch, monitoring must be intensified and measures adopted to reduce the level of nutrients in the main body of the Billings complex.