Jordan was late in adopting seawater and brackish water desalination as a source until the late 1990s and early 2000s. However, ongoing studies are still discussing the technical, economic, and socio-political aspects of brackish water reverse osmosis (BWRO) desalination plants. In this study, the water–energy nexus was considered, in order to highlight the main challenges facing BWRO desalination. We discuss the use of photovoltaic (PV) technology, together with BWRO desalination, as an approach to compensate for ecological, financial, and social challenges in Jordan. For this purpose, the performance of nine existing BWRO desalination plants in the agricultural, domestic, and industrial sectors is assessed. The water performance is assessed based on water consumption, safe yield extraction, plant recovery rate (R, %), and compliance to local and international water quality standards; the Specific Energy Consumption (SEC, kWh/m3) is taken as the main evaluation criterion to assess the energy performance of the BWRO desalination plants; and economic performance is assessed based on the overall cost of water produced per cubic meter (USD/m3). The main environmental component is the brine disposal management practice utilized by each plant. Based on this assessment, the main challenges in BWRO desalination are the unsustainable patterns of water production, mismanaged energy performance, low recovery rates, and improper brine disposal. The challenges in domestic and industrial BWRO desalination, which are completely dependent on the electricity grid, are associated with critical energy and costs losses, as reflected by the high SEC values (in the range of 2.7–5.6 kWh/m3) and high water costs per cubic meter (0.60–1.18 USD/m3). As such, the use of PV solar panels is suggested, in order to reduce the electricity consumption of the assessed BWRO plants. The installation of PV panels resulted in significantly reduced energy costs (by 69–74%) and total costs (by 50–54%), compared with energy costs from the electricity grid, over the lifetime of the assessed BWRO desalination plants.