Navy EOD provides support to a wide variety of "customers" including the realm of Special Operations and has task dedicated Navy Special Warfare units and some EOD folks are imbedded into NSW units. They also support other agencies/customers. From their official site:
The Navy's EOD force is organized at three levels: EOD Groups (EODGRUs), EOD Mobile Units (EODMUs), and various EOD Companies (EOD Companies)
EOD GROUPS
There are two EOD Groups: EODGRU ONE at San Diego, California (Naval Amphibious Base Coronado), and EODGRU TWO at Norfolk, Virginia (Naval Amphibious Base Little Creek). Both groups report to the Commander, Navy Expeditionary Combat Command.
EOD MOBILE UNITS
Each group has readiness responsibility for several subordinate EOD Mobile Units (EODMU). Though defensive in nature, EODMUs are trained in combative skills and small unit tactics. The pressures placed upon an EOD team can be enormous. Not only can they be called upon to disarm explosive ordnance and Improvised Explosive Devices (IEDs), but they may have to do so with enemy forces in close proximity. Regardless, EOD performs its mission when called upon.
EOD COMPANIES
These teams consist of several shore-based EOD companies supporting key naval installations along the east and west coasts of the United States and at selected locations inland and overseas. EODMUs are also comprised of deployable Mine Countermeasures Companies (EOD MCM Companies), multi-mission Mobile Companies (EOD MOB Companies), Naval Special Warfare Companies (NSW Companies), and Marine Mammal System Companies (MMS Companies).