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Managing ecosystems with deeply uncertain threshold responses and multiple decision makers poses nontrivial decision analytical challenges. The problem is imbued with deep uncertainties because decision makers do not know or cannot converge on a single probability density function for each key parameter, a perfect model structure, or a single adequate objective. The existing literature on managing multistate ecosystems has generally followed a normative decision-making approach based on expected utility maximization (MEU). This approach has simple and intuitive axiomatic foundations, but faces at least two limitations. First, a prespecified utility function is often unable to capture the preferences of diverse decision makers. Second, decision makers’ preferences depart from MEU in the presence of deep uncertainty. Here, we introduce a framework that allows decision makers to pose multiple objectives, explore the trade-offs between potentially conflicting preferences of diverse decision makers, and to identify strategies that are robust to deep uncertainties. The framework, referred to as many-objective robust decision making (MORDM), employs multiobjective evolutionary search to identify trade-offs between strategies, re-evaluates their performance under deep uncertainty, and uses interactive visual analytics to support the selection of robust management strategies. We demonstrate MORDM on a stylized decision problem posed by the management of a lake in which surpassing a pollution threshold causes eutrophication. Our results illustrate how framing the lake problem in terms of MEU can fail to represent key trade-offs between phosphorus levels in the lake and expected economic benefits. Moreover, the MEU strategy deteriorates severely in performance for all objectives under deep uncertainties. Alternatively, the MORDM framework enables the discovery of strategies that balance multiple preferences and perform well under deep uncertainty. This decision analytic framework allows the decision makers to select strategies with a better understanding of their expected trade-offs (traditional uncertainty) as well as their robustness (deep uncertainty).