## 3 Results  
### Site Characteristics  
During the deployment of the PAR light loggers, no fouling or sediment deposition was observed and therefore the difference in measured light availability between sites during submergence confirms a gradient in water column turbidity was captured across the six sites (PAR\({}_{\rm site}\); Figure 2A). Light availability was lowest at MNK-L and MNK-R with a median maximum daily PAR of 218 and 290 umol m\({}^{-2}\) s\({}^{-1}\), respectively. In addition, the interquartile range (IQR) was relatively low for both sites (297 and 365 umol m\({}^{-2}\) s\({}^{-1}\), respectively), which is suggestive of a consistently low light climate and thus high turbidity. RAG while having a similar IQR to both the MNK sites (283 umol m\({}^{-2}\) s\({}^{-1}\)), had a higher median maximum daily PAR of 500 umol m\({}^{-2}\) s\({}^{-1}\). In contrast, TAU-O, TAU-T and WTA had a considerably higher median maximum daily PAR (784-1140 m\({}^{-2}\) s\({}^{-1}\)), suggestive of overall less turbid water, and a high IQR (512-762 m\({}^{-2}\) s\({}^{-1}\)), indicative of intermittent increases in turbidity (rather than persistently high). Sediment surface PAR (PAR\({}_{\rm Sed}\)) measurements during submerged sampling periods suggest this gradient of water column turbidity was captured during each sampling event (Figure 2B-D). Where high incident light (PAR\({}_{\rm i}\)) occurred, greatest differences between PAR\({}_{\rm Sed}\) were observed at MNK-L, MNK-R and RAG. However, these differences are less pronounced with lower PAR\({}_{\rm i}\) values (e.g., during T2 sampling in winter).  
No consistent relationship was found between water column turbidity and sediment characteristics (Table 2). On average, mud content was relatively low (\(<\)4%) at MNK-R, TAU-T and WTA on all sampling dates. The highest mud content was recorded at RAG (maximum of 28%) with both MNK-L and TAU-O predominately \(>\)10%. Organic content was also relatively low at all sites (\(<\)5%) while median grain size (MGS) varied between sites (an average of 123 \(\upmu\)m in RAG to 248 \(\upmu\)m in WTA). Microalgal biomass (sediment chl \(a\) content) was highly variable with no clear relationship between sites or sampling dates. Univariate measures of macrofaunal community differed between sites (Table 2; see Tables A3 and A4 for community composition data). Most notable was the high abundance of _A. stutcluburyi_ (\(>\)50 core\({}^{-1}\)) at MNK-L, RAG and WTA which contributed to higher total macrofaunal abundance.  
Figure 2: Measured photosynthetically active radiation (PAR) at each site; **(A)** PAR\({}_{\text{Site}}\), daily maximum value over a 9-month period (March–November 2017), and during primary production measurements in **(B)** November 2017 (T1), **(C)** June 2018 (T2) and **(D)** November 2018 (T3). [PERSON] and blue bars indicate PAR\({}_{\text{i}}\) (incident, water surface) and PAR\({}_{\text{Sed}}\) (sediment surface), respectively, during submerged sampling periods. Red indicates PAR\({}_{\text{i}}\) during emerged sampling. Boxes represent the 25 th and 75 th percentiles, whiskers the 5 th and 95 th percentiles and a solid line within each box denotes the median.  
\begin{table}
\begin{tabular}{c c c c c c c c c c c c} \hline \multirow{2}{*}{**Site**} & \multirow{2}{*}{**Time**} & \multicolumn{4}{c}{**Sediment Properties**} & \multicolumn{4}{c}{**Toro**} & \multicolumn{2}{c}{**Microbytobntic**} & \multicolumn{2}{c}{**Macrofan**} & \multicolumn{2}{c}{**Community**} \\  & & & & & & & & & & & & \\  & **OC** & **Mad** & **MGS** & **NH\({}_{\textbf