*4.3. Water Quality and Sources of Nutrients in Timor-Leste*

The nutrient concentrations plus stable isotope ratios were more indicative of oceanic processes (upwelling, internal waves, etc.) than of terrestrially derived nutrient pollution. The levels of inorganic nutrients found in this study were not indicative of nutrient pollution. These values were comparable to nutrients measured in the Laclo river (~12 km east of Rural-E) in 2006 (See Supplementary Materials) [22]. Overall, nutrients were not found to be significantly elevated at surveyed sites. The sampling was also undertaken during the dry season (Mar to Nov) which would limit nutrient inputs from land and capturing elevated signals from point source pollution can be difficult.

Contrary to what was expected, combined nitrate and nitrite and phosphate averages were highest at Rural-N at 10 m; this could be a sign of upwelling nutrient-rich water [66,68,102,103,142]. Another source of nutrients at this depth could derive from submarine groundwater discharge [143]. An ephemeral bloom of cyanobacteria overgrowth was found at Urban-W 10 m in 2015 (6.1% prevalence), which can be a sign of elevated nutrients or other disturbances (ship strikes, etc.) [144–146]; however, seawater nutrients and stable isotope values were not elevated at this site suggesting the cause was not nutrient related. Although NH4 <sup>+</sup> was not significantly different between survey sites with the exception Rural-E 5 m, the range of 1.32 to 2.69 μM was greater than values between 0.3 μM and 2.2 μM [43,44,53] previously recorded for reefs in the Indo-Pacific.

The stable isotope data were consistent across sites and depths (range 2.5–5.5‰ excluding outliers) falling within the range of pristine oceanic (2–3‰) [48,147] and upwelling areas (5–6‰) [50,64–70]. The data were not indicative of δ15N sewage enrichment typically ranging from 8 to 22‰ [49,52,61,148,149]. The mean δ15N was significantly higher for the *Chlorodesmis* spp. at Urban-W as compared to Urban-E (Table 1). However, no *Chlorodesmis* spp. was found at Rural-N. *Halimeda* spp. were more abundant at sites and calcareous algae are good integrators of nitrogen over weeks to months versus days with fleshy macroalgae [60]. Similar values were recorded for both algae collected across sites and depths which indicates that the influx of nitrogen had been stable across several months. This is likely due to sampling being undertaken at the end of the dry season when there is little terrestrial runoff. There were a few outlier data points with much higher (12.17‰, 15.12‰) and lower (−6.79‰) <sup>δ</sup>15N values recorded in *Halimeda* samples, and these could be indicative of localized inputs on a scale of tens of meters of nutrients such as fish waste or groundwater discharge. Previous studies have demonstrated that macroalgal δ15N signatures decrease with depth where there is land-based pollution [50,52,57,150]. The influence of upwelling is less clear as both δ15N depletion and enrichment have been reported with upwelling [50,64,68,151].

In summary, assigning direct links between the condition of coral reefs and the source of nutrients is difficult. The mean δ15N values of algae sampled were higher than those reported from the open ocean. However, given the timing of collection, it is unlikely our sampling captured the effects of terrestrial run-off or of potential sewage pollution. Additionally, nutrients can be absorbed rapidly by biota and thus differences between pristine and polluted sites may not be readily apparent. Significant seasonal differences have been demonstrated for stable isotope values in macroalgae [51] so that further seasonal investigations are needed to elucidate the source of nutrients in nearshore waters.
