<p>The pond ecosystems provide habitats for diverse aquatic organisms, including fish and migratory birds, and held ecological, cultural, religious, aesthetic and touristic values. The main objective of this study is to evaluate the hydrochemistry and water quality including the controlling mechanisms of urban-based pond ecosystems in Kirtipur Municipality, Kathmandu, Nepal. The study adopted multivariate statistical techniques i.e., hierarchical cluster analysis (HCA), principal component analysis (PCA), discriminant analysis (DA) and geochemical indices to analyze hydrochemical characteristics of the ponds ecosystem. Results revealed alkaline pH in all the studied ponds and specific ionic order i.e., Ca²⁺  &gt; Mg²⁺  &gt; Na⁺  &gt; K⁺  &gt; Fe³⁺  &gt; NH₄⁺ and HCO₃⁻ &gt; Cl⁻ &gt; SO₄²⁻ &gt; NO₃⁻ &gt; PO₄³⁻ of major cations and anions, respectively. PCA identified four main components representing 75% of the variance, indicating multiple sources of the chemicals. HCA grouped the ponds into two major clusters based on their hydrochemical characteristics. DA successfully distinguished clusters with 97.5% of accuracy, revealing seven predictor variables as significant differentiators. These variables include water temperature, EC, TDS, total hardness, DO, K⁺ and NH₄⁺, highlighting their importance in discriminating between the two clusters. The water quality index of ponds ranged from 87 to 152. The Chiku and Diya ponds exhibited relatively better water quality, while others showed heavy pollution, primarily due to anthropogenic factors, indicating poor to unsuitable conditions. Aquaculture evaluation found that the majority of the studied ponds had unsatisfactory water quality for the same purpose. However, the irrigational water quality index met permissible limits. The study emphasizes the efficacy of multivariate techniques and geochemical indices for understanding water quality variation, providing insights for optimizing pond water resources and ensuring their sustainability.</p>