Farming in the Everglades Agricultural Area (EAA) of South Florida has long focused on nutrient management, particularly nitrogen (N) and phosphorus (P) utilization. The region’s organic soils (Histosols) provide natural fertility, but artificial drainage since the mid-20th century has accelerated soil oxidation, leading to subsidence. Nearly six feet of soil have been lost over the past century, making conservation practices essential to sustaining agriculture. Beneath these organic soils lies hard limestone bedrock, which complicates cultivation and water management as subsidence progresses. Additionally, sandy soils in the EAA have poor structure and are prone to nutrient leaching, impacting downstream water bodies, including Lake Okeechobee, Stormwater Treatment Areas, and the Florida Everglades. Sustainable agricultural practices are therefore critical to both soil conservation and water quality. Crop rotation is a recognized strategy for improving soil health, reducing erosion, and minimizing non-point source pollution. In the EAA, nearly 80% of farmland is dedicated to sugarcane, while the remaining 20% is rotated with winter vegetables and rice. Flooded rice rotations during summer alter soil redox conditions, potentially slowing soil subsidence. However, the full impact of crop rotation on soil and water quality remains underexplored. This four-year study evaluates the effects of sugarcane–flooded rice rotation versus continuous sugarcane on soil health and water quality in the EAA. Soil and water parameters will be monitored, and a Soil Health Index and Water Quality Index will be developed to compare different rotation systems. Additionally, soil depth surveys and remote sensing will be integrated to assess the relationship between soil depth and crop production. Findings will support conservation efforts, inform growers on sustainable practices, and contribute to broader watershed management initiatives in South Florida.