Draining parts of the western Scenic Rim, the creek's headwaters are in the Main Range National Park, a small sub-section of the Great Dividing Range. Its tributaries drain the slopes east of Toowoomba and areas to the north of. The total stream length of the Lockyer Creek network is. The total catchment area is, and covers nearly one quarter of the total catchment area of the Brisbane River. O'Reillys Weir is located about upstream from the creek's confluence with the Brisbane River. Approximately upstream from the junction of Lockyer Creek and the Brisbane River is the Wivenhoe Dam. Tributaries flowing into Lockyer Creek include Flagstone Creek, Sandy Creek, Alice Creek, Laidley Creek, Tenthill Creek, Murphys Creek and Ma Ma Creek. Lower areas of the catchment have been cleared for intensive agriculture. Upper parts of the catchment remain mostly forested, partially protected within Lockyer National Park formerly known as White Mountain State Forest. Bushfires, soil protection, water quality and flood management are the main resource management issues for the waterway. The creek is significantly degraded. The poor conditions have resulted in unstable stream banks and gully erosion from the removal of riparian vegetation. There are a total of nine major private and public water storages within this drainage system, including Atkinson Dam, Bill Gunn Dam and Lake Clarendon. The Lockyer Creek valley had been one of the driest catchments in Queensland during the recent droughts in Australia.
Flood events
During the 2011 Queensland floods, on 10 and 11 January the creek experienced severe flash flooding from overnight and daytime heavy rain in a catchment of about. During the floods the creek reached deep, a record that was higher than what was experienced during the 1974 Brisbane flood. The Bureau of Meteorology recorded a rise of in 23 minutes during the flash flood but initially dismissed the reading as a fault. It was estimated that 4,000 tonnes or of water per second flowed through Lockyer Creek, leading to the use of descriptive phrases such as "wall of water", or even "inland tsunami". Water rose approximately above the 1893 flood level recorded at the Lockyer Creek Railway bridge. A report by GHD Group for the Brisbane City Council suggested that flood mitigating dams on Lockyer Creek and Bremer River could be a useful measure for flood proofing Brisbane.
Bridges
The Lockyer Creek Bridge at Bageli Park, designed by William Pagan, is one of the largest of its type in Queensland and one of Australia's first reinforced concrete archrail bridges. The bridge, built in 1910/1911, features three spans, each supported by two arches, and appeared on a stamp that was part of a series featuring landmark bridges. A model of the bridge was featured in the April 2011 edition of the Australian Model Railway Magazine. The bridge is still used for very heavy Brisbane bound coal and grain traffic. Another single arch bridge on the same line, but over a side gully, with the same name, is closer to and was built in 1903. Further downstream in the district of Clarendon, an earlier railway structure built of timber piles with a deck of iron trusses, is possibly as spectacular. This bridge is no longer used by rail traffic.
Heritage listings
Lockyer Creek has a number of heritage-listed sites, including:
Toowoomba – Helidon Line: Lockyer Creek Railway Bridge
Toowoomba – Helidon Line: Lockyer Creek Railway Bridge