Once Rose Creek leaves the open plains of Rose Canyon, it traverses Interstate 5 and heads into dense Pacific Beach neighborhoods before it merges into Mission Bay. The portion of Rose Creek that rolls behind Mission Bay High School — the oasis of trees, shrubs and birds — makes for a lovely stroll but has become too clogged for the city to adequately control flooding. The city’s Storm Water Department is in the process of applying for a 20-year permit from state and federal agencies that will allow crews to clear vegetation out of channels like Rose Creek that threaten to flood development that was built too close to waterways.  “The city is looking at ways to preserve the larger trees to preserve the canopy but make sure the channel bottom is more clear of shrubs and scrubs that hold the water,” said environmental planner Bruce McIntyre for Helix Environmental Planning, a consultant to the city on the permitting process. “We’d like to keep the trees on the banks so there is still a habitat for birds to nest and rest in. We’ll look at each segment with a hydrology study to make sure we’re not taking out more than we need to.” Called the Master Storm Water System Maintenance Program (MSWSMP), the segments of creeks and channels pegged for clearing are detailed in the draft EIR that can be viewed at www.sandiego.gov/thinkblue (click on “Master Storm Water Maintenance Program EIR”). Comments for the draft EIR report are due by Aug. 22. If the permits are approved, work on the channels likely won’t begin until February of 2010. City crews once removed vegetation from waterways as part of routine maintenance, but in early 2000 state and federal agencies stepped in and wanted more oversight of the process, McIntyre said. Now the city must seek a permit under section 404 of the Clean Water Act that requires permission from agencies like the U.S. Army Corps of Engineers, California Department of Fish & Game, the California Regional Water Quality Control Board and the California Coastal Commission. In the interim, public works supervisor Bill Tanargo is having his crew remove couches, tables, chairs and bags of trash by hand from the ditch that runs behind Mission Bay High. Tanargo said the plan is to use mechanized equipment to remove all the vegetation from that portion of Rose Creek, unless something is protected, once the city receives the 20-year permit. “In the old days we’d put a bulldozer in there and clear everything. Now we’re much more sensitive to what we’re removing,” Tanargo said. “There are new guidelines on how we work.” The Master Storm Water System Maintenance Program covers a network of storm water facilities throughout San Diego that ranges from channels like Rose Creek to detention basins, pipes and culverts. According to the draft EIR for the program, removing vegetation could impact sensitive bird species like the least Bell’s vireo and southern willow flycatcher in wetlands, and the California gnatcatcher in areas of coastal sage scrub. State law requires the city to mitigate its impact to the wetlands, creeks and rivers affected by the flood control measures. In the case of Rose Creek, the city can either choose to “enhance” other portions of the creek by pulling weeds — often the invasive giant reed that resembles bamboo — every two years, or “restore” the area by removing invasive species and planting native vegetation in areas not troubled by flooding issues, such as within Rose Canyon. Choosing to mitigate through restoration is ultimately cheaper for the city, since it doesn’t have to pull weeds every two years, but is more costly upfront. “It costs $75,000 to remove weeds for two years, whereas it costs $200,000 to do the restoration,” McIntyre said. “If the city can find the money, we’d prefer to do the one-time mitigation.”