Wait a minute. . . First most of the waters in many of the rivers is covered by private oyster leases.
I will ask around about the rules of engagement relating to active aquaculture operations.
If you mean an oyster lease (which also means clams).
That only restricts the use of the bottom for raising clams and oysters (with an aquaculture permit) or to do the traditional way of placing shells or harvesting wild clams.
The only time that one MIGHT get in trouble is if you are working over an aquaculture operation (i.e. clams with mesh nets over them, or oysters in enclosures). Otherwise there is no restrictions to ANY other use of the water column for any reason. The only thing that is being leased is the bottom for the purpose of growing or harvesting clams or oysters.
You CAN set a gill net, crab pot, trot line on a leased area (with the possible exception of an aquaculture operation where they have structure that might be damaged by your use of the water column).
You CAN also anchor a boat in a leased area (with the possible exception of an aquaculture operation).
One of the things that is always brought up by applicants for cage on bottom aquaculture leases is that they act as fish attractants and that the fishing is better when they are there.
Here are the applicable regulations on aquaculture in Virginia.
4 VAC 20-335-10 PURPOSE.
The purpose of this regulation is to specify the criteria for shellfish aquaculture structures that may be employed on privately leased shellfish planting ground.
4 VAC 20-335-20 DEFINITIONS.
The following words and terms, when used in this regulation, shall have the following meaning unless the context clearly indicates otherwise:
"Commission" means the Marine Resources Commission.
"Shellfish" means native molluscan species or molluscan species imported in accordance with §28.2-825 of the Code of Virginia.
4 VAC 20-335-30 REQUIREMENTS AND CONDITIONS.
A. The activity must be conducted on planting ground leased in accordance with Chapter 6 of Title 28.2 of the Code of Virginia.
B. Leased planting ground must be properly marked in accordance with §28.2-607 and subsequent regulations (4 VAC20-290-10 et seq.).
C. In addition to the required marking of the boundary of the lease, the boundary of the area containing the structures shall be identified with markers meeting the description for markers identified in 4 VAC20-290-30 while structures are located on the bottom.
D. Any structures placed on the bottom must be non-toxic and shall not be known to leach any materials which would violate any water quality standards set by the Department of Environmental Quality.
E. Structures shall not extend higher than 12 inches above the bottom substrate.
F. No new structures shall be placed on existing stands of submerged aquatic vegetation.
G. No structures may cause more than a minimal adverse effect on navigation.
H. Shellfish must be harvested in accordance with all applicable laws and regulations.
I. The Commission may direct removal of any structures which fail to meet the requirements and conditions of this regulation.
Recreational aquaculture.4 VAC 20-336-10 AUTHORITY - EFFECTIVE DATE.
(a) This General Permit is promulgated pursuant to the authority contained in § 28.2-103 and Chapter 12 of Title 28.2 of the Code of Virginia.
(b) This General Permit conforms with current Commission policy in its establishment of general permits for projects which meet certain restrictive criteria.
(c) The effective date of this General Permit is January 1, 1998.
4 VAC 20-336-20 DEFINITIONS.
For the purposes of this general permit, riparian shellfish gardening is defined as the grow-out of native shellfish species in protective structures such as floats, bags, cages, etc. adjacent to a private, noncommercial pier or otherwise within a waterfront property owner's riparian area, exclusively for private, noncommercial purposes.
4 VAC 20-336-30 DISCUSSION.
(a) A principal objective of the permit streamlining efforts of this agency is the achievement of a single permit wherever possible for minor projects with minimal cumulative impacts.
(b) The Norfolk District of the U. S. Army Corps of Engineers has approved a Regional Permit (97-RP-19) for certain aquaculture/mariculture activities in waters of the Commonwealth of Virginia which are authorized by a local wetlands board or the Virginia Marine Resources Commission, or both.
4 VAC 20-336-40 PROCEDURES.
The Chief, Habitat Management Division, will administer the General Permit and assure:
(a) That the approved Local-State-Federal Permit Application form, or General Permit #3 Application Form, is completed and filed in accordance with the instructions contained therein.
(b) That aquaculture activities authorized by this permit achieve the policy and standards implicit in Chapter 12 of Title 28.2 of the Code of Virginia and reasonably accommodate guidelines promulgated by the Commission.
(c) That riparian shellfish gardening structures proposed meet the following criteria: (1) the proposed structures must be secured to a private pier which meets the criteria set forth in §28.2-1203 (5) of the Code of Virginia, or other duly authorized structure in such a manner that they do not adversely impact navigation and are wholly within the Permittee's riparian area, (2) shellfish grown in such structures will not be commercially marketed, (3) the Permittee shall be responsible for complying with Virginia Department of Health requirements and fisheries regulations regarding shellfish grown in condemned or otherwise restricted waters, (4) structures being used will not exceed 160 square feet in total area, (5) structures will be located so as not to impact existing stands of submerged aquatic vegetation (SAV).
(d) Projects which do not meet the criteria in (a) through (c) above will be processed for an individual permit with appropriate fees and royalties.
4 VAC 20-336-50 AUTHORIZATION AND CONDITIONS.
All proposals for noncommercial shellfish aquaculture structures to encroach in, on or over State-owned subaqueous land which meet the criteria in paragraph 4 (a) through (c) above are hereby approved subject to the following conditions:
(1) This permit grants no authority to the Permittee to encroach upon property rights, including riparian rights, of others.
(2) The duly authorized agents of the Commission shall have the right to enter upon the premises at reasonable times, for the purposes of inspecting the work being done pursuant to this permit.
(3) The Permittee shall comply with the water quality standards as established by the Department of Environmental Quality and all other applicable laws, ordinances, rules and regulations affecting the conduct of this project. The granting of this permit shall not relieve the Permittee of the responsibility of obtaining any and all other permits or authorization for this project.
(4) The permit shall not affect or interfere with the right vouchsafed to the people of Virginia concerning fowling and the catching of and taking of oysters and other shellfish in and from the waters not included within the terms of this permit.
(5) The Permittee shall, to the greatest extent practicable, minimize adverse impacts of the project on adjacent properties and wetlands and upon the natural resources of the Commonwealth.
(6) This permit may be revoked at any time by the Commission upon the failure of the Permittee to comply with the terms and conditions hereof or at the will of the General Assembly of Virginia.
(7) There is expressly excluded from this permit any portion of the waters within the Baylor Survey (Public Oyster Ground).
(

This permit is subject to any lease of oyster planting ground in effect on the date of this permit. Nothing in this permit shall be construed as allowing the Permittee to encroach on any lease without the consent of the leaseholder. The Permittee shall be liable for any damages to such lease.
(9) The issuance of this permit does not confer upon the Permittee any interest or title to the beds of the waters.
(10) All structures authorized by this permit which are not maintained in good repair or displaced to areas not authorized shall be completely removed from State-owned bottom within 30 days after notification by the Commission or its designated representatives.
(11) The Permittee agrees to indemnify and save harmless the Commonwealth of Virginia from any liability arising from the establishment, operation or maintenance of said project.
(12) This permit authorizes no claim to archaeological artifacts which may be encountered during the construction or operation of the project. If, however, archaeological remains are encountered, the Permittee agrees to notify the Commission, who will, in turn, notify the Virginia Department of Historic Resources. The Permittee further agrees to cooperate with agencies in the recovery of archaeological remains if deemed necessary.
(13) The Permittee agrees to respond to any inquiries or studies conducted by the Commission concerning the Permittee's aquaculture efforts.
(14) This General Permit shall remain valid for a period of five (5) years from the date of issuance. It may be extended upon a request from the applicant, provided the request is made prior to the permit expiration.
(15) This General Permit should be retained by the Permittee for the life of the project as evidence of authorization.
One last one on the second type of permit for aquaculture.4VAC20-1130-10. Purpose.
The purpose of this chapter is to establish a general permit for the use of temporary protective enclosures for the propagation of oysters and clams, including a notification process and special conditions necessary for the protection of public safety, navigation, natural resources, and the environment.
4VAC20-1130-20. Definitions.
The following words and terms, when used in this chapter, shall have the following meanings unless the context clearly indicates otherwise.
“Submerged aquatic vegetation” or “SAV” means any rooted, vascular submerged plants such as eelgrass (Zostera marine), widgeon grass (Ruppia maritima), or other species commonly found in the Chesapeake Bay and its tributaries.
“Temporary protective enclosure” means cage, rack, tray, or other similar device for holding and protecting oysters or clams.
4VAC20-1130-30. Notification Procedures.
A. All notifications for the use of temporary protective enclosures authorized by this general permit shall be made in writing to the Commissioner.
B. The notification shall contain the following information: the name, address and telephone number of the applicant, the location and plat file number depicted on an accurately scaled vicinity map, the approximate size of the area that will contain the temporary protective enclosures, the maximum number of structures to be placed on the leasehold at any given time, a detailed description of the temporary protective enclosures proposed to be deployed, the species to be cultured, a general description of the area within 500 feet of the lease boundary, including existing marine resources (SAV, shellfish beds, fixed fishing devices, traditional fishing and shellfish areas), locations of public and private piers and docks, water depths at mean low water, tidal range, the minimum vertical clearance, at mean low water, over the enclosures, the estimated date of placement of the structures, and any other information the Commissioner deems necessary to evaluate the proposal. Accurately scaled drawings shall be included with the notification, which depict the type of structures proposed to be deployed and the proposed deployment pattern. The notification shall also include a list of the names and addresses of all riparian property owners within 500 feet of the area containing the temporary protective enclosures and shall depict the location of their land on a tax map or other suitable map. Riparian Property Owner Acknowledgement Forms for such riparian property owners, may be included with the notification. Such forms shall be signed by the riparian property owner and shall indicate their comments on the notification. Should such forms not be provided in the notification, the Commissioner, or his designee, shall notify the adjacent property owners of the pending notification.
C. The Commissioner, or his designee, shall determine that the notification is complete and filed in accordance with the instructions contained therein.
D. The Commissioner will provide written notice to the leaseholder of his final action on the proposal.
E. In accordance with the provisions of §28.2-603.2 of the Code of Virginia, the Commissioner may approve the proposal, approve the proposal with conditions, or deny the proposal, of the leaseholder. The Commissioner may prescribe conditions for any proposal for the protection of public safety, navigation, natural resources, and the environment, that include, but are not limited to: the type of construction materials used for the temporary enclosures; the manner in which such structures are deployed; the distances the structures are placed from the shoreline, navigable channels, piers, wharfs, or other water dependent facility; and the minimum vertical clearance at mean low water over any temporary structure. When determining these conditions, the Commissioner shall also consider those factors set forth in Section 28.2-1205 A. of the Code of Virginia.
4VAC20-1130-40. General Conditions.
A. The general permit established by this chapter grants no authorizations to the permittee to encroach upon the property rights, including riparian rights, of others.
B. Authorized agents of the Commission shall have the right to enter upon the premises at reasonable times, for the purpose of inspecting the work being done pursuant to this permit.
C. This general permit shall not be transferred without written consent of the Commissioner.
D. The permittee shall, minimize the adverse effects of the project upon adjacent properties and wetlands and upon the natural resources of the Commonwealth.
E. This permit may be revoked at any time by the Commissioner upon the failure of the permittee to comply with any of the terms and conditions hereof.
F. There is expressly excluded from the permit any portion of the waters within the boundaries of the Baylor Survey.
G. The issuance of this permit does not confer upon the Permittee any interest or title to the beds or waters of the Commonwealth.
H. All structures authorized by this permit which are not maintained in good repair shall be completely removed from State-owned bottom within five business days after written notification by the Commissioner.
I. This permit authorizes no claim to archaeological or historic artifacts which may be encountered during the the placement of temporary protective enclosures. If, however, archaeological remains are encountered, the Permittee agrees to notify the Commissioner, who will, in turn notify the Department of Historic Resources and Virginia Institute of Marine Science. The Permittee further agrees to cooperate with agencies of the Commonwealth in the recovery of archaeological remains if deemed necessary.
J. The Permittee agrees to indemnify and save harmless the Commonwealth of Virginia from any liability arising from the establishment, operation or maintenance of said project.
K. The public shall not be excluded from any space not physically occupied by the authorized temporary protective enclosures.
L. This permit does not obviate the need to obtain other federal, state, or local authorizations required by law or regulation.
4VAC20-1130-50. Special Conditions.
A. The Permittee authorized by this chapter shall hold a current Oyster or Clam Aquaculture Product Owners Permit, issued by the Commission, shall be in compliance with the provisions of Regulation 4VAC20-610-10 et seq., “Pertaining to Mandatory Harvest Reporting”, and shall have paid all fees, costs, and the annual rent for the oyster ground lease. Failure to pay all fees and rents as required by §§ 28.2-608 and 28.2-612 of the Code of Virginia and failure to report as required in 4VAC20-610-10 et seq. may result in termination of the lease and general permit.
B. Any temporary protective enclosure shall be constructed of non-toxic materials.
C. No temporary protective enclosure shall be placed in or upon submerged aquatic vegetation beds, and consideration, by the Commissioner, for authorizing the placement of protective enclosures in currently un-vegetated areas that are documented as historically supporting SAV beds, shall include consultation with the Virginia Institute of Marine Science, in order to determine the potential for impacts on SAV, within the term of the prospective lease. If SAV colonizes within the boundaries of the area designated for the temporary protective enclosures, the authorization for those structures under this general permit shall remain in effect only for the remainder of the term of the lease. The general permit shall be renewed only upon a finding by the Commissioner that the placement of the temporary protective enclosures, within the lease, will not significantly interfere with the continued vitality of the SAV.
D. No individual temporary protective enclosure shall exceed 70 cubic feet, in volume.
E. Temporary protective enclosures may be placed individually on the bottom, placed in racks, or stacked one on top of another.
F. Temporary protective enclosures shall not be placed within any marked navigation channel, or in any area that would create a hazard.
G. Temporary protective enclosures shall not be placed in any area that would impede customary access to navigable waters, from any riparian property, public or commercial landing, or marina facility.
H. Temporary protective enclosures shall not be placed within 100 feet of any shoreline or pier without the agreement of the riparian property owner.
I. Temporary protective enclosures shall be placed in a manner that allows for their ease of access, maintenance, and removal and shall not exceed an average of 250 individual structures per acre within the permitted area or 250 arrays of structures, when those enclosures are stacked one on top of another.
J. In addition to the marking of the boundary of the lease, required by Regulation 4VAC20-335-10 et seq., the boundary of the area containing the structures shall be identified with markers meeting the description for markers identified in Regulation 4VAC20-290-30, while structures are located on the bottom. At intervals no smaller than 150 feet and along the perimeter of the area containing the temporary protective enclosures, the leaseholder shall place placards, constructed of a durable material, which shall be at least four feet above the mean high water line, and shall conform to the description established by the Commissioner.
K. No temporary protective enclosure shall be marked by more than one buoy, which shall not exceed 15 inches in its longest dimension. The Commissioner may designate the color of the buoys used for marking temporary protective enclosures.
L. Nothing in this general permit shall authorize the placement of any temporary protective enclosure designed to float on the surface of the water.
M. Leaseholders shall, within five business days, remove any enclosure that is not actively in use for the planting and propagating of shellfish, and, upon expiration or termination of a lease, or of the leaseholder’s Aquaculture Product Owner’s Permit, the leaseholder shall promptly remove all enclosures placed on the leasehold.
N. Leaseholders shall maintain a list identifying those leases on which enclosures are placed during the terms of the lease and provide, upon request, a current copy of the list to authorized representatives of the Commission. Leaseholders shall also submit such list to be filed with any application for lease renewal made pursuant to §28.2-613 of the Code of Virginia.
O. The Commissioner, at his discretion, may order the immediate removal or relocation of any enclosure that interferes with navigation, creates a hazard, or otherwise fails to comply with the conditions of the general permit.
4VAC20-1130-60. General Permit Fees.
A. A. Upon approval of the notification to use temporary protective enclosures, the applicant shall pay to the Commission the following fee:
1. For up to 500 structures, $125.00.
2. For over 500 but not more than 1000 structures, $250.00.
3. For over 1000 but not more than 2500 structures, $625.00.
4. For over 2500 structures, $1000.00.
B. The fee established by this section shall be paid annually by the leaseholder, on or before the anniversary date of the issuance of the general permit.