This is a GREAT topic.
While our company is headquartered in Arkansas, where the stormwater regulations are relatively lax, we have 6 other offices around the country and our top clients develop sites in all 50 states. Many of our engineering staff maintain additional certifications as required by certain states (such as Georgia and California) and are well versed in the practice of erosion prevention and sediment control. Our larger clients have developed internal processes and standards for their Civil consultants to provide a SWPPP document in addition to meeting the AHJ's erosion and sediment control plan standards. These SWPPP documents are often included directly in the specifications for the project, becoming part of the contract documents. Several of them are operating under consent decrees from the federal level so this type of control was necessary to avoid further fines and liability. In contrast, others have learned from those who have developed before them and have never been fined for stormwater compliance. Our firm is often hired by the Owner to review stormwater documents (both SWPPP and plans) prepared by other civil consultants. A pretty nice master service agreement.
While SWPPP documents often border on means and methods they are intended to express an idea of preventing erosion and controlling sediment on the site. The design-bid-build project is a 3 part effort with the Owner, Engineer, and Contractor all serving vital roles under the EJCDC. The SWPPP allows the Contractor to make changes to the erosion control plans and directs him to document the change. Furthermore, the SWPPP often incorporates a multitude of other studies and determinations the contractor is often not qualified to make. In my experience when the Contractor hires an Engineer to inspect his work, or produce documents which he must adhere to, there is created a potential conflict of interest. This is why Section 17 of the IBC requires the Design Professional in Responsible Charge to submit a statement of special inspections and those inspections must be paid for by the Owner, not the Contractor (recent initiatives in the city of Tulsa, OK point to this becoming more frequently enforced). But I digress.
Regarding the NOI; many state's permits require the Owner to sign and certify the NOI & SWPPP because ultimately the Owner holds the checkbook for the project and has the most skin in the game. While the contractor is often identified as a co-permittee, the Owner is often fined when things go wrong (see consent decree). Some states additionally require the Engineer to prepare, sign, and seal the NOI and perform periodic inspections of the erosion and sediment control measures implemented on the site. Where post construction stormwater management is also required, these inspections along with a final as-built certification are used to release the certificate of occupancy for the building. In an ideal job the Owner and Engineer would be on site with enough frequency to identify problem areas and prevent potential violations. However, this often leads to excessive cost (especially when the Owner and Engineer are not local to the job-site). Smaller job-sites often do not require production of SWPPP documents or filing of an NOI (size and requirement varies by state and municipality). This does not relieve the contractor from implementing BMPs and meeting the intent of the state or federal general stormwater permit.
Ultimately, it is the responsibility of all three parties to ensure compliance of the project.
For what it's worth, our company signs and seals every SWPPP we produce.
Nate the Great