Climate patterns in the agricultural zones of the Indus basin are predicted to undergo undesirable changes in the hydrological cycle. These changes are a threat to the widespread agricultural activity and associated livelihoods of the underlying population. Livestock, an essential sector for human sustenance in the basin, is also a major source of greenhouse gas emissions thereby contributing towards climate change. However, it is also a recipient of climate impacts, thus introducing feedbacks and uncertainties that are further accentuated by the Water-Energy-Food Nexus. Here we model and simulate the farm-level dairy operations of a single dairy farm by introducing informatics-driven precision measurements of water, energy, food, and carbon emissions in a system dynamics framework. We analyze the simulated trajectories for energy, water, and waste fluxes to under different interventive scenarios to identify actions that enhance productivity and minimize environmental impact. The model is constructed based on data gathered from two dairy farms located in rural Punjab, Pakistan. The farms have a livestock capacity of 300 and 134 animals respectively, with data related to water, energy, food, and climate gathered over a duration of two years. The simulated results may be used to uncover structural changes in dairy-farm operations which improve the economic structure of the farm while remining within the thresholds defined by Sustainable Development Goals (SDG) 3, 7 and 13 set by the United Nations. The model itself also helps in unravelling the complex interactions among water-energy-food flows along with their coupling to land-climate interactions in context of the dairy farm operations. Beyond the climate change adaptation measures extracted from this study, the system dynamics model that we construct in the process, can help develop economic tools that leverage the advantages of water/climate informatics driven data services and decisions under large variabilities to devise sound agricultural policy.