This division monitors and improves Manatee County's stormwater system, while ensuring FEMA floodplain compliance. Stormwater Engineering is involved with capital improvement projects, including state and federal grant writing. This section is responsible for inspecting and reporting of county-maintained stormwater facilities for the National Pollutant Discharge Elimination System (NPDES) permit compliance for the Environmental Protection Agency (EPA) and re-certification of stormwater section of the Community Rating System (CRS) program through the Federal Emergency Management Agency (FEMA).

Stormwater Engineering also reviews No-Rise Certificates and floodplain compensation calculations. Additionally, Stormwater Engineering conducts floodplain studies with Southwest Florida Watershed Management District (SWFWMD), and oversees the floodplain map revisions prepared for and adopted by the Board of County Commissioners.

Stormwater Engineering also maintains several near real-time stream elevation and rain sensor systems: Monitor Real Time Rain and Stream Gauges