## 2 Materials and Methods
### Data Analysis  
Submerged dissolved O2 and emerged CO2 fluxes were estimated from the change in concentration during the incubation period and corrected for the chamber area and volume. Submerged O2 fluxes were not corrected for water column processes owing to the small contribution relative to benthic production/respiration (<5% of the measured chamber flux, data not presented). A respiratory quotient of 1 was used to convert CO2 consumption and production measurements to O2 production and consumption, respectively. This value is likely to be realistic for well-oxygenated sediments with low mud and organic content [42], such as those within this study. Light chamber fluxes were equivalent to net primary production (NPP; umol O2 m-2 h-1) and dark chamber fluxes to sediment oxygen consumption (SOC). The sum of these two fluxes from paired chambers within a plot provided an estimate of gross primary production (GPP). A productivity/respiration (p/r) ratio was calculated for each chamber, as defined by [PERSON] and [PERSON] [43]: (hourly productivity (GPP) \(\times\) daylight period)/(hourly respiration \(\times\) 24 h), to estimate if the sediments were net autotrophic (p/r \(>\) 1; more carbon is produced than respired), or net heterotrophic (p/r \(<\) 1; more carbon is respired than produced). Odyssey PAR logger data were converted from count measurements to PAR (umol m-2 s-1) by a calibrated regression with a LI-COR PAR sensor prior to deployment. Three values of PAR are used throughout this study: site PAR (PARSite), incident PAR (PARi) and sediment surface PAR (PARSed). PARSite is used as a proxy for site turbidity as described above, where a higher PARSite value indicates lower site turbidity. The other two PAR measurements correspond to those taken during sampling and are used for normalising rates of primary production. PARi describes light received at the sediment surface during emerged incubations and at the water surface during submerged incubations. Whereas PARSed refers to light received at the sediment surface during the submerged incubations and therefore accounts for water column attenuation. GPP was first normalised by PARi (GPPi) to account for variability in light intensities between sampling dates while retaining attenuation effects of the water column (e.g., from turbidity). GPP was additionally normalised by PARSed and photosynthetic biomass (sediment chl \(a\) i.e., productivity per unit of photosynthesising biomass [18]) to determine photosynthetic efficiency (GPPSed + chla). To determine if nutrient enrichment influenced primary production estimates and if this differed between sites and sampling events, a preliminary analysis using repeated measures PERMANOVA was conducted. For submerged fluxes, nutrient enrichment (3 levels), site (6 levels) and time (2 levels; T1 and T3) were set as fixed factors and replicate plot nested within treatment. T2 was omitted because measurements were only made at 3 of the 6 sites. For emerged fluxes, site was reduced to 3 levels (RAG, TAU-O, TAU-T) and time included T2 and T3 (Figure 1, Table 10). These analyses revealed high spatial and temporal variability. This was expected due to the extent of the experiment (6 different sites within 4 estuaries, over 20 months) which spanned a range of environmental conditions expected to influence primary production. To differentiate between this natural heterogeneity (in both time and space) and reveal any potential treatment effects, submerged and emerged primary production estimates (NPP and GPP) were normalised by an average of the control plot values. This resulted in treatment effect size being relative to the site-specific background level and sampling date. Control normalised (CN) submerged and emerged primary production estimates were tested for differences from control values (i.e., NPPCN, GPPCN \(\
eq\) 1) using one-sample _t_-tests.