Tropical maar lakes are distinct ecosystems with unique ecological features. To comprehend, manage, and conserve these lakes, it is essential to understand their water sources, particularly groundwater, and the hydrogeochemical processes shaping their water chemistry. This research focuses on the maar lake Alchichica in central Mexico, known for harboring 18 new and endemic species and a ring of stromatolites. With groundwater discharge as the primary source, concerns arise over anthropic extraction impacts on water levels and stromatolite survival. Sampling six wells and one piezometer revealed major ion (Ca²⁺, Mg²⁺, K⁺, Na⁺, Cl⁻, HCO₃⁻, SO₄²⁻) and trace element (Fe, Al³⁺, SiO₂) concentrations. Geochemical evolution was explored through diagrams, geological sections, and inverse geochemical models using the PHREEQC code. Findings indicate groundwater evolving along controlled flow paths, and influencing chemical composition through water–rock interactions. The lake’s unique conditions, resulting from the mixing of two flows, enable stromatolite formation. Water level reduction appears unrelated to evaporation at the sampled sites, suggesting a need for a broader study in a larger area. Analyzing the maar lake’s hydrochemistry provides valuable insights into unique characteristics supporting high endemism in this ecosystem. This research enhances our understanding of groundwater’s geochemical processes and hydrogeochemical evolution in maar lakes, with potential applications worldwide.