System models have been used to improve water management and environmental decision making. In spite of the many existing mathematical models and tools that attempt to improve environmental decision making, few efforts have been made to identify how scarce resources (e.g., water, budget) can be more efficiently allocated to improve the environmental and ecological performance of different ecosystems (e.g., wetland habitat). This dissertation presents a set of management tools to improve the environmental and ecological performance. These tools are described in three studies. First, a simple optimization model is developed to help regulators and watershed managers determine cost-effective best management practices (BMPs) to reduce phosphorus load at the Echo Reservoir Watershed, Utah. The model minimizes the costs of BMP implementation to achieve a specified phosphorus load reduction target. Second, a novel approach is developed to quantify wetland habitat performance. This performance metric is embedded in a new optimization model to recommend water allocations and invasive vegetation control in wetlands. Model recommendations are subject to constraints such as water availability, spatial connectivity of wetland, hydraulic infrastructure capacities, vegetation growth and responses to management, plus financial and time resources available to allocate water and invasive vegetation control. Third, an agent-based model is developed to simulate the spread of the invasive Phragmites australis (common reed), one of the most successful invasive plant species in wetlands. Results of the agent-based model are embedded into an optimization model (developed in the second study) to recommend invasive vegetation control actions. The second and third studies were applied at the Bear River Migratory Bird Refuge, which is the largest wetland complex on the Great Salt Lake, Utah. These three studies provide a set of decision-support tools that recommend: (1) BMPs to reduce phosphorus loading in a watershed, (2) management strategies to improve wetland bird habitat, and (3) control strategies to minimize invasive Phragmites spread. Together, these models provide important insights and recommendations for managers to make informed decisions to manage excess nutrients in water bodies as well as to improve wetland management.