Assessment of water quality evolution in the thousands of existing and future mine pit lakes worldwide requires new numerical tools that integrate geochemical, hydrological, and biological processes. A coupled model was used to test alternative hypothesized controls on water quality in a pit lake over ∼8 years. The evolution of pH, Al, and Fe were closely linked; field observations were reproduced with generic solubility equilibrium controls on Fe(III) and Al and a commonly reported acceleration of the abiotic Fe(II) oxidation rate by 2-3 orders of magnitude. Simulations indicated an ongoing acidity loading at the site, and the depletion of Al mineral buffering capacity after ∼5 years. Simulations also supported the existence of pH limitation on nitrification, and a limitation on phytoplankton growth other than the commonly postulated P and DIC limitations. Furthermore, the model reproduced the general patterns of salinity, pH, Al, and Fe during an uncontrolled river breach in 2011, however, incorporating sediment biogeochemical feedbacks is required to reproduce the observed postbreach internal alkalinity generation in the lake. The modeling approach is applicable to the study of hydrological, geochemical, and biological interactions for a range of lake and reservoir management challenges.