Public access and use of Rookery Bay National Estuarine Research Reserve (RBNERR) lands, when compatible with DEP and RBNERR management goals, is an important component of the mission of RBNERR. Compatible public use for RBNERR is primarily defined as passive and low-impact to ensure continued long-term preservation of essential coastal resources. With the exception of recreational fishing and commercial harvest, allowed public use within RBNERR is non-consumptive.

One of RBNERR's critical management challenges is balancing significant increases in public use with the need to protect natural and cultural resources. RBNERR is located in one of the fastest growing metropolitan areas in the nation, leading to increased pressure for recreational opportunities. Primary public use of RBNERR resources has traditionally been boating and fishing, but other uses are rising. Initial steps taken by RBNERR to promote compatible public use include the construction of trails and boardwalks, installation of informational signage, conducting workshops, seminars and courses for the general community and targeted users (e.g. inshore fishing interests).

Despite these efforts, incompatible public use resulting in destruction or degradation of natural resources is increasing within RBNERR. Over the last 20 years, RBNERR has experienced a significant increase in manatee mortality from boating. Use of personal watercraft, airboats and similar shallow draft vessels has increased significantly, providing motorized access to shallow waters and submerged resources of RBNERR that have not previously been impacted. Wading bird colonies have been disturbed by boaters moving into such close proximity that the birds are flushed from their sites. Recreational boaters are using RBNERR waters more frequently for overnight anchorages. These can contribute to degraded water quality with waste discharges, and impacts to submerged resources from anchoring. Off-road vehicle use in upland/wetland areas can cause rutting and sheetflow disturbances. Areas within RBNERR that experience the highest level of intensive public use currently include South Key Island, Shell Island Road and seasonal use of barrier islands (e.g., camping) in the Ten Thousand Islands.

These challenges will require continued education and outreach efforts to encourage coastal stewardship. Monitoring public use and their impacts on natural resources is also necessary to determine appropriate management methods.