Assessments are used to fund the day-to-day maintenance of the levees, pump stations, small capital projects, and first response activity during a flood emergency for those who reside within the boundaries of RD1000. Property assessments are collected by the local property taxing authority, the Sacramento County Tax Collector, and the Sutter County Tax Collector.

The assessment for each property is determined by its location, the size of the parcel, its land use (eg: residential, commercial, industrial, or agricultural), and the relative benefit assigned to that land use. 

A typical single-family home on an urban residential lot will pay $10 per year; reduced in 2023 at the decision of the Board of Trustees from the previous minimum amount of $25 per year per the Water Code; for essential direct public safety benefits to all residents located within district boundaries. The District is divided into several geographic zones of benefit based on the potential depth of flooding should the perimeter levee system fail as well as interior drainage services provided by the District. The District's annual operations and maintenance costs are spread proportionally among the properties within Natomas.