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We describe the application of Bayesian hierarchical models to the analysis of data from long-term, environmental monitoring programs. The goal of these ongoing programs is to understand status and trend in natural resources. Data are usually collected using complex sampling designs including stratification, revisit schedules, finite populations, unequal probabilities of inclusion of sample units, and censored observations. Complex designs intentionally create data that are missing from the complete data that could theoretically be obtained. This “missingness” cannot be ignored in analysis. Data collected by monitoring programs have traditionally been analyzed using the design-based Horvitz–Thompson estimator to obtain point estimates of means and variances over time. However, Horvitz–Thompson point estimates are not capable of supporting inference on temporal trend or the predictor variables that might explain trend, which instead requires model-based inference. The key to applying model-based inference to data arising from complex designs is to include information about the sampling design in the analysis. The statistical concept of ignorability provides a theoretical foundation for meeting this requirement. We show how Bayesian hierarchical models provide a general framework supporting inference on status and trend using data from the National Park Service Inventory and Monitoring Program as examples. Supplemental Materials Code and data for implementing the analyses described here can be accessed here: https://doi.org/10.36967/code-2287025.