Mangrove sediments can act as sources of the greenhouse trace gases, nitrous oxide (N2O) and methane (CH4). Confident reporting of trace gas emissions from mangrove sediments at local levels is important for regional emissions inventories, since small changes in N2O and CH4 fluxes greatly influence greenhouse gas budgets due to their high global warming potentials. It is also important to identify the drivers of trace gas emission, to prioritise management for minimising emissions. We measured N2O and CH4 fluxes and abiotic sediment parameters at midday low tide in winter and summer seasons, at four sites (27°33′S, 152°59′E) ranging from estuary to ocean sub-tropical mangrove sediments, having varied anthropogenic impacts. At all sites, sediment N2O and CH4 emissions were significantly lower during winter (7–26 μg N2O m−2·h−1; 47–466 μg CH4 m−2·h−1) compared to summer (28–202 μg N2O m−2·h−1; 247–1570 μg CH4 m−2·h−1). Sediment temperature, ranging from 18 to 33 °C, strongly influenced N2O and CH4 emissions. Highest emissions (202 μg N2O m−2·h−1, 1570 μg CH4 m−2·h−1) were detected at human-impacted estuary sites, which generally had higher total carbon (<8%) and total nitrogen (<0.4%) in sediments and reduced salinity (<16 dS·m−1). Large between-site variation highlights the need for regular monitoring of sub-tropical mangroves to capture short-lived, episodic N2O and CH4 flux events that are affected by sediment biophysico-chemical conditions at site level. This is important, particularly at sites receiving anthropogenic nutrients, and that have variable freshwater inputs and tidal hydrology.