*2.1. Study Site*

Timor-Leste is a small island country located inside the southern edge of the CT and between Australia and Indonesia (Figure 1). The country gained its independence in 2002 following nearly 25 years of Indonesian occupation. It lies within the Indonesian ThroughFlow (ITF), a major oceanographic feature connecting the Pacific and Indian Oceans. The ITF transports an estimated 4.9 Sverdrups (106 m3/s) of water through the Ombai Strait along the north coast (Figure 1) [81–85].

This study was undertaken along the coast of Dili, Timor-Leste to complement a growing body of coral reef science undertaken in the area. Previous indications of reef health in this area have typically been anecdotes from surveys with other objectives. Dili, the capital (8◦33 S and 125◦34 E), houses a quarter of the country's population, with 252,884 people recorded in the 2015 Census [86]. The Northwest monsoon season extends from December to May, when there is more rain and greater runoff to the coast [87]. The seasonal Comoro River runs through Dili, with flows ranging from less than 0.5 m3/s from July to November, to 12.3 m3/s in March [20]. Timorese waters are affected by semi-diurnal tides with a range of 1–2 m along the north coast [88]. The present study was conducted in two, three-week field trips that occurred in the dry season in 15–27 November 2015 and

15–29 June 2017. The dry, Northwest monsoon season offers safer surveying conditions but would also limit terrestrial run-off inputs such as nutrients.

**Figure 1.** Timor-Leste lies between Indonesia and Australia within the Indonesian ThroughFlow (ITF). Arrows indicate inflows and outflows of the ITF adapted from [81,82]. The yellow dashed box indicates the Lesser Sunda Islands (adapted from [85]). Enlarged map on the right shows the location of the survey sites in Timor-Leste near the capital of Dili. Survey sites are Rural-N on Ataúro Island in the Ombai Strait, Rural-E 40 km east of Dili, and Urban-W and Urban-E flanking Dili. The highly seasonal Comoro River can be seen just east of Urban-W (in Dili) and the Laclo River east of Rural-E. The four sites were sampled on two occasions in November 2015 and June 2017. Jaco Island lies at the easternmost point of the country.

Surveys were conducted at four sites; two sites flanking Dili were representative of reefs under urban influences ("Urban-W" with 4993.0 people/km2; "Urban-E" with 449.8 people/km2) and two sites were representative of reefs under rural influences ("Rural-N" 30.7 people/km2, and "Rural-E" with 34.9 people/km2 [86]; Figure 1). Sites were chosen for logistics and to complement NOAA data collected between 2012 and 2016 [89].
