## Materials and Methods
### Data Handling and Statistics  
Single and interactive effects of warming (ambient and warm), HBCDD addition (with HBCDD and without HBCDD), abiotic variables, and phyto- and zooplankton species abundances, were assessed using constrained analysis of principle coordinates (CAP), based on Bray-Curtis dissimilarities. Prior to testing the effects of temperature and HBCDD addition and abiotic variables on species abundances of both phyto-, and zooplankton, species matrices were fourth root transformed to account for homoscedasticity and to downweigh the importance of taxa with very high abundances. Additionally, the abiotic variables were tested for autocorrelation between predictor variables and factors and no autocorrelation was found. Furthermore, the effect of the blocks (i.e., troughs) was tested, but since it did not have an effect, it was removed from the analyses. All multivariate analyses were performed in R version 3.2. [22]. The model for phytoplankton included both factors of warming and HBCDD addition as single and interactive effects, as well as all abiotic variables chlorophyll a, phosphate (PO\({}_{4}\)), total nitrogen, P/R ratios, and pelagic primary production, with the holding times (t6 and t13) constant. Significance of the model, terms, and axis were assessed using a permutation procedure with 999 permutations. The minimal adequate model (containing only significant parameters \(\alpha=0.05\)) was identified through step-wise deletion of non-significant parameters [23]. The analyses were performed using the \"capscale\" function from the {vegan} R package [24]. A similarity percentage test (SIMPER) was used to identify which phytoplankton species drove the community-level effects, using significant factor(s). For the zooplankton species matrix, both the abiotic variables (same as above) as well as all phytoplankton species were used as predictors. The analysis was then performed the same way as described for the phytoplankton species abundance. Three-way ANOVA (factors: time, temperature, HBCDD) was used to test for: differences in pelagic and benthic primary production (standardized to average A\(-\) at each time point to remove the effect of differences in light intensities during incubations at the different time points), total N, and PO\({}_{4}\)\({}^{-}\) concentrations in the water. Homogeneity of variance was tested using [PERSON]'s test and non-homogeneous data was Box-Cox transformed where necessary. The analyses were performed in Statistica version 12.5 (Dell Inc., Tulsa, OK, USA). Since too few benthic community data were available for a meaningful benthic CAP analysis, and several benthic endpoints were only measured at one time point, benthic parameters were analyzed using correlation analysis and ANOVA. Two-way ANOVA (factors: temperature, HBCDD) was used to test for differences in: abundance of each meiofauna taxa at t13; abundance of Hydrobiidae at t6; _L. ballhica_ biomass per cosm at t6 and t13. Homogeneity of variance was tested using [PERSON]'s test and non-homogeneous data were square-root transformed where necessary. To investigate potential connections between the benthic and pelagic components of the ecosystem, two multiple correlations were performed (t6 and t13 separately) on the following data: abundances of the 5 phytoplankton and 6 zooplankton groups identified by SIMPER (see above) to cumulatively contribute to 70% of the dissimilarity between treatments in the pelagic analysis; pelagic and benthic primary production; chlorophyll a, total N, and PO\({}_{4}\) concentrations. For t6, the number of Hydrobiidae was also available. For the t13 data correlation, the following variables were also available: total number of meiofauna, numbers of Turbellaria and _Microarthridion littorale_, and total biomass of _L. ballhica_. Although the focus of this analysis was benthic-pelagic linkages, it was also used to help explain the relationships between plankton species. The significance of the correlation coefficients r was tested using a two-tailed \(t\) test.