The upper reaches of the river including its headwaters are totally in the Connetquot River State Park Preserve or Lakeland County Park before it becomes an estuary.

It starts just south of the Long Island Expressway from springs in the Lakeland County Park in Islandia where it is called Connetquot Brook.

The estuary portion south of Sunrise Highway at Oakdale is officially called the Connetquot River although in popular usage both the brook and river share the same name.

The entire Connetquot River watershed habitat represents the largest undeveloped contiguous area within Suffolk County that covers an entire river watershed.

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